Variant report

Variant	rs11974980
Chromosome Location	chr7:150009838-150009839
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:150004469..150007293-chr7:150009416..150012608,5	K562	blood:
2	chr7:150008263..150011121-chr7:150102492..150104771,2	K562	blood:
3	chr7:150009392..150012620-chr7:150013659..150016251,3	MCF-7	breast:
4	chr7:150005819..150007873-chr7:150009129..150011102,2	K562	blood:
5	chr7:150007648..150010098-chr7:150018612..150020930,2	MCF-7	breast:
6	chr7:150009132..150011651-chr7:150053831..150057388,3	K562	blood:

Variant related genes	Relation type
ENSG00000127399	Chromatin interaction
ENSG00000106526	Chromatin interaction
ENSG00000196456	Chromatin interaction

Extended variants
information (count: 68 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10247016	0.83[CHB][hapmap]
rs10952249	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10952250	0.85[CEU][hapmap];0.85[CHB][hapmap];0.95[CHD][hapmap];0.94[MEX][hapmap];0.94[TSI][hapmap];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11764936	0.85[CEU][hapmap];0.88[MEX][hapmap];0.89[TSI][hapmap];0.85[EUR][1000 genomes]
rs11765644	0.85[EUR][1000 genomes]
rs11765692	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11766288	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11767726	0.95[CEU][hapmap];0.85[CHB][hapmap];0.87[CHD][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11769348	0.85[CEU][hapmap];0.88[MEX][hapmap];0.89[TSI][hapmap];0.85[EUR][1000 genomes]
rs11773351	0.83[EUR][1000 genomes]
rs11975886	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11983355	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1464752	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1464753	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17173681	0.80[CEU][hapmap]
rs17173682	0.80[CEU][hapmap]
rs17837498	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1916932	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1962004	0.93[CEU][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1983440	0.85[CEU][hapmap];0.85[CHB][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2108851	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2108852	0.95[CEU][hapmap];0.85[CHB][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2108853	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2108854	0.95[CEU][hapmap];0.85[CHB][hapmap];0.90[CHD][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2159234	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2159235	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2159236	0.94[CEU][hapmap];0.83[CHB][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2373751	0.85[EUR][1000 genomes]
rs3088207	0.83[EUR][1000 genomes]
rs3735167	0.80[CEU][hapmap];0.83[TSI][hapmap]
rs3735169	0.84[CEU][hapmap];0.83[EUR][1000 genomes]
rs3735170	0.84[CEU][hapmap];0.83[EUR][1000 genomes]
rs3735171	0.84[CEU][hapmap];0.84[EUR][1000 genomes]
rs3735172	0.85[CEU][hapmap];0.95[CHD][hapmap];0.94[MEX][hapmap];0.94[TSI][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3735173	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3735174	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3735175	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3757423	0.84[MEX][hapmap]
rs3800780	0.85[EUR][1000 genomes]
rs3800781	0.85[EUR][1000 genomes]
rs4395803	0.85[EUR][1000 genomes]
rs4554381	0.85[CEU][hapmap];0.83[CHB][hapmap];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs55715989	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55881542	0.85[EUR][1000 genomes]
rs56019796	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56190213	0.85[EUR][1000 genomes]
rs56402329	0.81[EUR][1000 genomes]
rs56923535	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56998970	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs57888387	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs59572505	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs60268791	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs60283368	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs60467296	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73170169	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs73170174	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73170185	0.85[EUR][1000 genomes]
rs7781827	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7788316	1.00[CEU][hapmap];0.90[CHB][hapmap];0.91[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7800196	0.80[CEU][hapmap]
rs7806429	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv889435	chr7:149585379-150013393	ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv1034409	chr7:149844639-150447071	Flanking Active TSS Active TSS Genic enhancers Enhancers ZNF genes & repeats Bivalent Enhancer Weak transcription Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
3	nsv608990	chr7:149961274-150707488	Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
4	nsv1015582	chr7:149967986-150285104	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
5	nsv508490	chr7:150006068-150051241	Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
6	nsv889453	chr7:150009838-150104410	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers 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 target site	50 gene(s)	inside rSNPs	diseases
7	nsv889454	chr7:150009838-150115183	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases

mRNA abundance (count:15)

SNP	Gene	Cis/trans	Tissue	Source
rs11974980	ZBED6CL	cis	Esophagus Muscularis	GTEx
rs11974980	ZBED6CL	cis	Esophagus Mucosa	GTEx
rs11974980	C7orf29	Cis_1M	lymphoblastoid	RTeQTL
rs11974980	LRRC61	cis	Muscle Skeletal	GTEx
rs11974980	LRRC61	cis	Thyroid	GTEx
rs11974980	RARRES2	cis	multi-tissue	Pritchard
rs11974980	LRRC61	cis	Adipose Subcutaneous	GTEx
rs11974980	LRRC61	cis	Nerve Tibial	GTEx
rs11974980	LRRC61	cis	lung	GTEx
rs11974980	LRRC61	Cis_1M	lymphoblastoid	RTeQTL
rs11974980	LRRC61	cis	Skin Sun Exposed Lower leg	GTEx
rs11974980	LRRC61	cis	Esophagus Mucosa	GTEx
rs11974980	LRRC61	cis	Whole Blood	GTEx
rs11974980	REPIN1	cis	Muscle Skeletal	GTEx
rs11974980	LRRC61	cis	Artery Tibial	GTEx

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:149984200-150012400	Weak transcription	Liver	Liver
2	chr7:149984200-150019400	Weak transcription	Colonic Mucosa	Colon
3	chr7:149992400-150018000	Weak transcription	Fetal Intestine Small	intestine
4	chr7:150003800-150016000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr7:150004000-150019000	Weak transcription	Primary hematopoietic stem cells	blood
6	chr7:150005200-150010000	Weak transcription	HepG2	liver
7	chr7:150007000-150010200	Enhancers	Hela-S3	cervix
8	chr7:150007000-150015000	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr7:150007600-150018000	Weak transcription	Fetal Intestine Large	intestine
10	chr7:150008000-150010400	Enhancers	Fetal Muscle Leg	muscle
11	chr7:150008400-150010200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
12	chr7:150008400-150010400	Enhancers	HSMMtube	muscle
13	chr7:150008400-150011200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr7:150008600-150011000	Weak transcription	Gastric	stomach
15	chr7:150008800-150010600	Enhancers	HSMM	muscle
16	chr7:150008800-150011400	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
17	chr7:150008800-150011600	Enhancers	HUES48 Cell Line	embryonic stem cell
18	chr7:150008800-150011600	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
19	chr7:150009000-150010000	Weak transcription	Pancreas	Pancrea
20	chr7:150009000-150010200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr7:150009000-150010400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr7:150009000-150010400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr7:150009000-150010600	Enhancers	HUES64 Cell Line	embryonic stem cell
24	chr7:150009000-150011400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
25	chr7:150009200-150010000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr7:150009200-150010200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr7:150009200-150010200	Weak transcription	Fetal Kidney	kidney
28	chr7:150009200-150010800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr7:150009200-150011000	Enhancers	ES-I3 Cell Line	embryonic stem cell
30	chr7:150009200-150011000	Weak transcription	Spleen	Spleen
31	chr7:150009200-150011400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr7:150009400-150010200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr7:150009400-150017000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
34	chr7:150009400-150020000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr7:150009600-150010000	Weak transcription	H1 Cell Line	embryonic stem cell
36	chr7:150009600-150010000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr7:150009600-150010000	Weak transcription	H9 Cell Line	embryonic stem cell
38	chr7:150009600-150010400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr7:150009600-150010400	Enhancers	NHLF	lung
40	chr7:150009600-150010600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr7:150009600-150011600	Enhancers	iPS-20b Cell Line	embryonic stem cell
42	chr7:150009600-150016000	Weak transcription	GM12878-XiMat	blood
43	chr7:150009800-150010000	Enhancers	K562	blood
44	chr7:150009800-150010400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
45	chr7:150009800-150014800	Weak transcription	NH-A	brain
46	chr7:150009800-150017000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--

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