Variant report

Variant	rs11973498
Chromosome Location	chr7:2886873-2886874
allele	A/C
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	STAT3	chr7:2886743-2886878	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:2884125..2886886-chr7:2909522..2911680,2	MCF-7	breast:
2	chr7:2882986..2886273-chr7:2886531..2891062,6	MCF-7	breast:

Variant related genes	Relation type
GNA12	TF binding region
ENSG00000146535	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs1182143	0.82[CEU][hapmap]
rs1182155	0.95[CEU][hapmap];0.87[EUR][1000 genomes]
rs1182174	0.85[CEU][hapmap];0.80[EUR][1000 genomes]
rs1182183	0.82[CEU][hapmap]
rs1182198	0.82[CEU][hapmap]
rs1182199	0.82[EUR][1000 genomes]
rs12700373	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13230946	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13230995	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1614791	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1636247	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1636248	0.91[ASN][1000 genomes]
rs1636249	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1636250	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1636251	0.94[ASN][1000 genomes]
rs1636252	0.96[ASN][1000 genomes]
rs1636253	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1636254	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1636255	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1636256	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1636264	0.82[CEU][hapmap];0.82[EUR][1000 genomes]
rs1639034	0.97[ASN][1000 genomes]
rs1639036	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1639040	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1639066	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1713912	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1713921	0.92[ASN][1000 genomes]
rs2107964	0.86[CEU][hapmap]
rs2527677	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2527680	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2527681	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2533867	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2533868	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2533870	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2533871	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2533875	0.93[ASN][1000 genomes]
rs2533877	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2533878	0.82[EUR][1000 genomes]
rs2533889	0.82[EUR][1000 genomes]
rs2533891	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2644281	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs2644286	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2644293	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2644300	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2644309	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2679259	0.97[ASN][1000 genomes]
rs71522301	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs71522302	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs71524003	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7783400	1.00[CEU][hapmap];0.90[CHB][hapmap];0.89[JPT][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1015700	chr7:2753965-2945848	Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv1022612	chr7:2789555-3019200	Enhancers ZNF genes & repeats Genic enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	nsv1018162	chr7:2817460-2891181	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
4	nsv538655	chr7:2817460-2891181	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
5	nsv887313	chr7:2875420-2927120	Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
6	nsv887314	chr7:2875420-2944187	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription 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	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs11973498	GNA12	cis	Artery Tibial	GTEx
rs11973498	GNA12	cis	Esophagus Muscularis	GTEx
rs11973498		cis	Lymphoblastoid	GTEx
rs11973498	GNA12	cis	multi-tissue	Pritchard
rs11973498	GNA12	Cis_1M	lymphoblastoid	RTeQTL
rs11973498	GNA12	cis	Nerve Tibial	GTEx

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:2884600-2889600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr7:2884600-2889600	Weak transcription	Fetal Kidney	kidney
3	chr7:2884600-2896000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr7:2884600-2902800	Weak transcription	Right Ventricle	heart
5	chr7:2884800-2887800	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr7:2884800-2887800	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr7:2884800-2889600	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr7:2884800-2889800	Weak transcription	Fetal Brain Male	brain
9	chr7:2884800-2889800	Weak transcription	Pancreas	Pancrea
10	chr7:2884800-2890600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr7:2884800-2891000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr7:2884800-2891200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr7:2884800-2891200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr7:2884800-2895800	Weak transcription	Fetal Heart	heart
15	chr7:2885000-2887200	Weak transcription	Duodenum Mucosa	Duodenum
16	chr7:2885000-2889600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr7:2885000-2889800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
18	chr7:2885000-2890400	Weak transcription	Dnd41	blood
19	chr7:2885000-2891000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
20	chr7:2885000-2902000	Weak transcription	Primary hematopoietic stem cells	blood
21	chr7:2885800-2887400	Weak transcription	HepG2	liver
22	chr7:2886600-2887800	Enhancers	Rectal Mucosa Donor 31	rectum
23	chr7:2886600-2888000	Enhancers	Fetal Intestine Small	intestine
24	chr7:2886800-2887400	Enhancers	Fetal Intestine Large	intestine

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