Variant report

Variant	rs4980524
Chromosome Location	chr11:63959259-63959260
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:63958164..63961175-chr11:64073026..64075417,3	MCF-7	breast:
2	chr11:63957637..63959858-chr11:64001168..64003198,2	MCF-7	breast:
3	chr11:63955085..63958830-chr11:63958900..63961430,4	MCF-7	breast:
4	chr11:63920929..63923512-chr11:63957225..63959261,2	MCF-7	breast:
5	chr11:63958665..63961367-chr11:63992375..63994620,2	MCF-7	breast:
6	chr11:63949462..63951169-chr11:63959042..63961813,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000256116	Chromatin interaction
ENSG00000149743	Chromatin interaction
ENSG00000149761	Chromatin interaction
ENSG00000173511	Chromatin interaction
ENSG00000173153	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs11231722	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11603192	0.80[CHB][hapmap]
rs11603538	0.92[YRI][hapmap];0.87[AFR][1000 genomes]
rs12362602	0.88[EUR][1000 genomes]
rs12418535	0.81[CHB][hapmap]
rs12787945	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17699798	0.87[EUR][1000 genomes]
rs1860368	0.83[JPT][hapmap]
rs2236647	0.96[CEU][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2236648	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2282492	0.80[CHB][hapmap];0.83[JPT][hapmap]
rs2429455	0.88[YRI][hapmap]
rs2515241	0.81[CHB][hapmap];0.92[YRI][hapmap];0.86[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs2701533	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2845597	0.80[CHB][hapmap];0.92[YRI][hapmap];0.91[AFR][1000 genomes]
rs2875748	0.88[CEU][hapmap];0.84[EUR][1000 genomes]
rs4980508	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs4980525	0.82[CEU][hapmap]
rs594942	0.88[YRI][hapmap]
rs627055	0.81[CEU][hapmap]
rs645461	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7112960	0.80[CHB][hapmap]
rs7938819	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7948329	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs882147	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:21 , 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	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
20	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
21	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4980524	TRPT1	cis	Muscle Skeletal	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:63954600-63960000	Weak transcription	Gastric	stomach
2	chr11:63954600-63967400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr11:63954800-63960000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr11:63954800-63960000	Weak transcription	Aorta	Aorta
5	chr11:63955000-63959400	Weak transcription	Psoas Muscle	Psoas
6	chr11:63955000-63959600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr11:63955000-63960000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr11:63955000-63960000	Weak transcription	Esophagus	oesophagus
9	chr11:63955000-63960600	Weak transcription	Fetal Kidney	kidney
10	chr11:63955000-63969400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr11:63955200-63959400	Weak transcription	Ovary	ovary
12	chr11:63955200-63959600	Weak transcription	NHEK	skin
13	chr11:63955200-63959800	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr11:63955200-63959800	Weak transcription	Right Ventricle	heart
15	chr11:63955200-63960000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr11:63955200-63960000	Weak transcription	Rectal Smooth Muscle	rectum
17	chr11:63955200-63960000	Weak transcription	HSMMtube	muscle
18	chr11:63955200-63960000	Weak transcription	NHDF-Ad	bronchial
19	chr11:63955200-63960400	Weak transcription	HMEC	breast
20	chr11:63955200-63960800	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
21	chr11:63955200-63971600	Strong transcription	Fetal Intestine Small	intestine
22	chr11:63955200-63974400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr11:63955200-63975000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
24	chr11:63955200-63975200	Strong transcription	HUES64 Cell Line	embryonic stem cell
25	chr11:63955400-63959800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr11:63955400-63959800	Weak transcription	Primary hematopoietic stem cells	blood
27	chr11:63955400-63960000	Weak transcription	Rectal Mucosa Donor 29	rectum
28	chr11:63955400-63960000	Weak transcription	HUVEC	blood vessel
29	chr11:63955400-63960400	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr11:63955400-63962000	Weak transcription	Small Intestine	intestine
31	chr11:63955800-63960600	Genic enhancers	Primary T helper cells PMA-I stimulated	--
32	chr11:63955800-63971200	Strong transcription	Fetal Stomach	stomach
33	chr11:63955800-63975400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr11:63956000-63959800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr11:63956000-63960800	Genic enhancers	Primary T cells fromperipheralblood	blood
36	chr11:63956000-63973600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr11:63956200-63959400	Weak transcription	Sigmoid Colon	Sigmoid Colon
38	chr11:63956200-63959800	Weak transcription	NHLF	lung
39	chr11:63956200-63960000	Weak transcription	Primary B cells from cord blood	blood
40	chr11:63956200-63960000	Weak transcription	Colonic Mucosa	Colon
41	chr11:63956200-63960000	Weak transcription	Left Ventricle	heart
42	chr11:63956200-63960000	Weak transcription	Skeletal Muscle Male	skeletal muscle
43	chr11:63956200-63962000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr11:63956200-63964000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr11:63956200-63974200	Weak transcription	Right Atrium	heart
46	chr11:63956400-63959800	Weak transcription	Muscle Satellite Cultured Cells	--
47	chr11:63956400-63960000	Weak transcription	H9 Cell Line	embryonic stem cell
48	chr11:63956400-63960000	Weak transcription	Brain Substantia Nigra	brain
49	chr11:63956400-63960000	Weak transcription	Skeletal Muscle Female	skeletal muscle
50	chr11:63956400-63970200	Weak transcription	Stomach Mucosa	stomach

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