Variant report

Variant	rs12802950
Chromosome Location	chr11:63965771-63965772
allele	A/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr11:63965448-63966118	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:63951087..63956474-chr11:63963164..63967847,7	MCF-7	breast:
2	chr11:63932754..63935809-chr11:63963316..63968184,5	MCF-7	breast:

Variant related genes	Relation type
STIP1	TF binding region
ENSG00000133315	Chromatin interaction
ENSG00000168439	Chromatin interaction

Extended variants
information (count: 77 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs1058735	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1059440	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11231701	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11601024	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11601577	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11602181	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11603212	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11605738	0.82[AFR][1000 genomes]
rs11606544	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11607007	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11607144	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11607165	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12418035	0.81[EUR][1000 genomes]
rs12574258	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12575642	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12787852	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12794145	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12797120	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12798333	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2001003	0.81[AMR][1000 genomes]
rs2015226	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2070765	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2154986	0.82[EUR][1000 genomes]
rs2282490	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2875749	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34089806	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34113693	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34838337	0.81[EUR][1000 genomes]
rs35090903	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35095324	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35458188	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35524387	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35858916	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3802933	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3824854	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs58632573	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6591837	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs66648159	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs67546972	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7102327	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7111278	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs7112277	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7130030	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs71479474	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72918475	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72920332	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72922039	0.81[AMR][1000 genomes]
rs7478730	0.82[AFR][1000 genomes]
rs7939784	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7944061	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7952318	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs882146	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:25 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv897631	chr11:63664882-64129722	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	254 gene(s)	inside rSNPs	diseases
2	esv1802079	chr11:63746066-64151373	Bivalent Enhancer Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	247 gene(s)	inside rSNPs	diseases
3	nsv897646	chr11:63754986-64150370	Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	245 gene(s)	inside rSNPs	diseases
4	nsv1035875	chr11:63800238-64132030	Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	234 gene(s)	inside rSNPs	diseases
5	nsv469961	chr11:63822940-64085967	Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Enhancers Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	224 gene(s)	inside rSNPs	diseases
6	nsv897660	chr11:63860826-64125142	Weak transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	231 gene(s)	inside rSNPs	diseases
7	nsv897661	chr11:63863405-64129722	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	233 gene(s)	inside rSNPs	diseases
8	nsv897662	chr11:63889749-64150370	Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	237 gene(s)	inside rSNPs	diseases
9	nsv897664	chr11:63919742-64150370	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	237 gene(s)	inside rSNPs	diseases
10	nsv468592	chr11:63924446-64042997	Enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	166 gene(s)	inside rSNPs	diseases
11	nsv555184	chr11:63924446-64042997	Genic enhancers Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	166 gene(s)	inside rSNPs	diseases
12	nsv897665	chr11:63927695-64026144	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	155 gene(s)	inside rSNPs	diseases
13	nsv897666	chr11:63929493-64026144	Enhancers Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	155 gene(s)	inside rSNPs	diseases
14	nsv869944	chr11:63932152-64123062	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	227 gene(s)	inside rSNPs	diseases
15	nsv468593	chr11:63941734-64089874	Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	212 gene(s)	inside rSNPs	diseases
16	nsv555185	chr11:63941734-64089874	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	212 gene(s)	inside rSNPs	diseases
17	nsv555186	chr11:63949095-64097233	Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	212 gene(s)	inside rSNPs	diseases
18	nsv468595	chr11:63953121-64027888	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	146 gene(s)	inside rSNPs	diseases
19	nsv555187	chr11:63953121-64027888	Strong transcription Weak transcription Transcr. at gene 5' and 3' Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	146 gene(s)	inside rSNPs	diseases
20	nsv897667	chr11:63964657-64078380	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	141 gene(s)	inside rSNPs	diseases
21	nsv897668	chr11:63964657-64085298	Weak transcription Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	163 gene(s)	inside rSNPs	diseases
22	nsv897669	chr11:63964657-64089874	Genic enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	164 gene(s)	inside rSNPs	diseases
23	nsv897670	chr11:63964657-64097233	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	164 gene(s)	inside rSNPs	diseases
24	nsv897671	chr11:63964657-64150370	Active TSS Flanking Active TSS Genic enhancers Weak transcription Enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	179 gene(s)	inside rSNPs	diseases
25	nsv825943	chr11:63965453-63967699	Weak transcription Strong transcription Genic enhancers	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	n/a

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12802950	TRPT1	cis	Muscle Skeletal	GTEx
rs12802950	PPP1R14B	cis	Heart Left Ventricle	GTEx
rs12802950	PPP1R14B	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:63954600-63967400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr11:63955000-63969400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr11:63955200-63971600	Strong transcription	Fetal Intestine Small	intestine
4	chr11:63955200-63974400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr11:63955200-63975000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
6	chr11:63955200-63975200	Strong transcription	HUES64 Cell Line	embryonic stem cell
7	chr11:63955800-63971200	Strong transcription	Fetal Stomach	stomach
8	chr11:63955800-63975400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr11:63956000-63973600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr11:63956200-63974200	Weak transcription	Right Atrium	heart
11	chr11:63956400-63970200	Weak transcription	Stomach Mucosa	stomach
12	chr11:63957000-63970600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr11:63957000-63971200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr11:63957000-63971400	Strong transcription	Fetal Muscle Trunk	muscle
15	chr11:63957200-63965800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
16	chr11:63957400-63971000	Strong transcription	Dnd41	blood
17	chr11:63957400-63972000	Strong transcription	Cortex derived primary cultured neurospheres	brain
18	chr11:63957400-63974800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr11:63957400-63975800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr11:63957600-63970400	Strong transcription	Fetal Thymus	thymus
21	chr11:63958200-63971200	Strong transcription	Hela-S3	cervix
22	chr11:63959200-63972200	Strong transcription	Lung	lung
23	chr11:63959400-63966000	Strong transcription	Monocytes-CD14+_RO01746	blood
24	chr11:63959400-63971600	Strong transcription	Placenta	Placenta
25	chr11:63959400-63972000	Strong transcription	Sigmoid Colon	Sigmoid Colon
26	chr11:63959400-63972000	Strong transcription	Thymus	Thymus
27	chr11:63959600-63966400	Strong transcription	Ovary	ovary
28	chr11:63959600-63966400	Strong transcription	HSMM	muscle
29	chr11:63959600-63971400	Strong transcription	A549	lung
30	chr11:63959600-63975000	Strong transcription	NHEK	skin
31	chr11:63959600-63976000	Strong transcription	Fetal Brain Female	brain
32	chr11:63959600-63977000	Strong transcription	iPS-15b Cell Line	embryonic stem cell
33	chr11:63959800-63965800	Strong transcription	Primary monocytes fromperipheralblood	blood
34	chr11:63959800-63966200	Strong transcription	K562	blood
35	chr11:63959800-63966400	Strong transcription	NHLF	lung
36	chr11:63959800-63967800	Strong transcription	Liver	Liver
37	chr11:63959800-63971000	Strong transcription	GM12878-XiMat	blood
38	chr11:63959800-63971600	Strong transcription	Primary T killer memory cells from peripheral blood	blood
39	chr11:63959800-63971600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr11:63959800-63971600	Strong transcription	Muscle Satellite Cultured Cells	--
41	chr11:63959800-63971600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr11:63959800-63971800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr11:63959800-63971800	Strong transcription	Primary T cells from cord blood	blood
44	chr11:63959800-63971800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr11:63959800-63971800	Strong transcription	Adipose Nuclei	Adipose
46	chr11:63959800-63971800	Strong transcription	Duodenum Smooth Muscle	Duodenum
47	chr11:63959800-63971800	Strong transcription	Stomach Smooth Muscle	stomach
48	chr11:63959800-63971800	Strong transcription	Osteobl	bone
49	chr11:63959800-63973400	Strong transcription	Right Ventricle	heart
50	chr11:63959800-63976000	Strong transcription	HUES48 Cell Line	embryonic stem cell

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