Variant report

Variant	rs11604782
Chromosome Location	chr11:63946650-63946651
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:63929801..63939249-chr11:63945151..63958671,77	MCF-7	breast:
2	chr11:63929784..63936274-chr11:63944807..63955078,25	K562	blood:
3	chr11:63941163..63943232-chr11:63946290..63948899,3	K562	blood:
4	chr11:63941531..63943845-chr11:63945242..63947346,2	MCF-7	breast:
5	chr11:63944790..63948071-chr11:64005777..64008701,3	MCF-7	breast:
6	chr11:63931311..63936745-chr11:63945647..63958123,49	MCF-7	breast:
7	chr11:63940462..63942702-chr11:63944754..63946922,2	K562	blood:
8	chr11:63932221..63937015-chr11:63943035..63946757,7	K562	blood:

No data

Variant related genes	Relation type
ENSG00000173486	Chromatin interaction
ENSG00000133315	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs11601522	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11603042	0.93[YRI][hapmap];0.81[EUR][1000 genomes]
rs11603192	0.92[CEU][hapmap];0.83[CHB][hapmap];0.93[JPT][hapmap];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11603384	1.00[CEU][hapmap];0.89[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11603538	0.92[CEU][hapmap];0.94[JPT][hapmap];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12418535	0.92[CEU][hapmap];0.84[CHB][hapmap];0.94[JPT][hapmap];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12420070	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1860368	0.92[CEU][hapmap];0.87[JPT][hapmap];0.92[EUR][1000 genomes]
rs2282491	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2282492	0.88[CEU][hapmap];0.83[CHB][hapmap];0.87[JPT][hapmap];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2429455	0.92[CEU][hapmap];0.80[JPT][hapmap];0.91[EUR][1000 genomes]
rs2515241	0.92[CEU][hapmap];0.84[CHB][hapmap];0.94[JPT][hapmap];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2845597	0.92[CEU][hapmap];0.83[CHB][hapmap];0.93[JPT][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3741404	0.88[YRI][hapmap];0.83[EUR][1000 genomes]
rs3888316	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs594461	0.80[CEU][hapmap]
rs594942	0.88[CEU][hapmap];0.89[CHB][hapmap];0.82[JPT][hapmap];0.83[EUR][1000 genomes]
rs595880	0.83[EUR][1000 genomes]
rs604203	0.86[YRI][hapmap]
rs60452247	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs638227	0.81[CEU][hapmap]
rs640999	0.81[CEU][hapmap]
rs641430	0.80[CEU][hapmap]
rs651855	0.80[CEU][hapmap]
rs6591836	0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7102177	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7111753	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7112960	0.92[CEU][hapmap];0.83[CHB][hapmap];0.93[JPT][hapmap];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:19 , 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	nsv832185	chr11:63819946-63963532	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	89 gene(s)	inside rSNPs	diseases
6	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
7	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
8	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
9	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
10	nsv897663	chr11:63910153-63962152	Weak transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	86 gene(s)	inside rSNPs	n/a
11	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
12	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
13	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
14	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
15	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
16	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
17	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
18	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
19	esv33971	chr11:63946624-63946699	Weak transcription Strong transcription Enhancers ZNF genes & repeats	Chromatin interactive region	2 gene(s)	inside rSNPs	n/a

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11604782	TRPT1	cis	Heart Left Ventricle	GTEx
rs11604782	TRPT1	cis	Muscle Skeletal	GTEx
rs11604782	NUDT22	Cis_1M	lymphoblastoid	RTeQTL
rs11604782	PPP1R14B	cis	Muscle Skeletal	GTEx

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:63934200-63948000	Weak transcription	Right Ventricle	heart
2	chr11:63934200-63948200	Weak transcription	Brain Angular Gyrus	brain
3	chr11:63934200-63948200	Weak transcription	Esophagus	oesophagus
4	chr11:63934200-63948200	Weak transcription	Stomach Mucosa	stomach
5	chr11:63934200-63948800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr11:63934200-63950800	Weak transcription	Gastric	stomach
7	chr11:63934400-63948000	Weak transcription	Right Atrium	heart
8	chr11:63935000-63948200	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr11:63935800-63947400	Weak transcription	Stomach Smooth Muscle	stomach
10	chr11:63935800-63948000	Weak transcription	Pancreas	Pancrea
11	chr11:63937600-63946800	Weak transcription	A549	lung
12	chr11:63941400-63948200	Weak transcription	Brain Substantia Nigra	brain
13	chr11:63941600-63946800	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr11:63941600-63949000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr11:63941800-63948000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr11:63941800-63948200	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr11:63942000-63948000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr11:63942400-63948200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr11:63943200-63949000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr11:63943400-63948200	Weak transcription	Aorta	Aorta
21	chr11:63943600-63948200	Weak transcription	NHLF	lung
22	chr11:63943600-63951000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
23	chr11:63943800-63946800	Weak transcription	Fetal Muscle Trunk	muscle
24	chr11:63944000-63948000	Weak transcription	HSMMtube	muscle
25	chr11:63944600-63948200	Weak transcription	Thymus	Thymus
26	chr11:63944600-63949000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
27	chr11:63944800-63948000	Weak transcription	Brain Hippocampus Middle	brain
28	chr11:63944800-63948000	Weak transcription	Left Ventricle	heart
29	chr11:63944800-63948000	Weak transcription	HSMM	muscle
30	chr11:63944800-63948400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr11:63944800-63948400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr11:63944800-63948800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
33	chr11:63944800-63948800	Weak transcription	Primary T helper cells PMA-I stimulated	--
34	chr11:63944800-63948800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
35	chr11:63944800-63950600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
36	chr11:63945000-63947200	Weak transcription	Primary T cells from cord blood	blood
37	chr11:63945000-63948200	Weak transcription	Primary T cells fromperipheralblood	blood
38	chr11:63945000-63948400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
39	chr11:63945000-63948600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
40	chr11:63945000-63948600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
41	chr11:63945000-63948800	Weak transcription	Primary T helper cells fromperipheralblood	blood
42	chr11:63945000-63949000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
43	chr11:63945000-63949000	Weak transcription	Dnd41	blood
44	chr11:63945000-63952000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
45	chr11:63945200-63947200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
46	chr11:63945400-63947400	Strong transcription	Fetal Muscle Leg	muscle
47	chr11:63945400-63948200	Weak transcription	Fetal Thymus	thymus
48	chr11:63945400-63948400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr11:63945400-63948400	Weak transcription	Fetal Kidney	kidney
50	chr11:63945600-63948000	Weak transcription	Brain Inferior Temporal Lobe	brain

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