Variant report

Variant	rs1636252
Chromosome Location	chr7:2884993-2884994
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	RFX5	chr7:2882892-2885962	SK-N-SH	brain:	n/a	n/a
2	BHLHE40	chr7:2883910-2885058	K562	blood:	n/a	chr7:2883924-2883940 chr7:2883916-2883932
3	GATA2	chr7:2884130-2885050	SH-SY5Y	brain:	n/a	chr7:2884409-2884425 chr7:2884407-2884428 chr7:2884411-2884423 chr7:2884565-2884572 chr7:2884412-2884421 chr7:2884403-2884420
4	MXI1	chr7:2883299-2885027	IMR90	lung:	n/a	n/a
5	GATA3	chr7:2884873-2885061	SH-SY5Y	brain:	n/a	n/a
6	TCF7L2	chr7:2884664-2885248	MCF-7	breast:	n/a	n/a
7	BHLHE40	chr7:2884806-2884996	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr7:2884125..2886886-chr7:2909522..2911680,2	MCF-7	breast:
2	chr1:149858014..149859677-chr7:2882924..2885730,2	MCF-7	breast:
3	chr7:2869377..2877481-chr7:2880306..2885399,15	MCF-7	breast:
4	chr7:2878232..2880029-chr7:2884178..2886023,2	MCF-7	breast:
5	chr7:2726313..2732670-chr7:2878755..2886203,10	MCF-7	breast:

Variant related genes	Relation type
GNA12	TF binding region
ENSG00000174945	Chromatin interaction
ENSG00000178096	Chromatin interaction
ENSG00000184260	Chromatin interaction
ENSG00000184270	Chromatin interaction
ENSG00000184678	Chromatin interaction
ENSG00000231357	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs1182156	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11973498	0.96[ASN][1000 genomes]
rs12700373	0.95[ASN][1000 genomes]
rs13230995	0.96[ASN][1000 genomes]
rs1614791	0.94[ASN][1000 genomes]
rs1623138	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1636247	0.91[ASN][1000 genomes]
rs1636248	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1636249	0.97[ASN][1000 genomes]
rs1636250	0.97[ASN][1000 genomes]
rs1636251	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1636253	0.96[ASN][1000 genomes]
rs1636254	0.96[ASN][1000 genomes]
rs1636255	0.94[ASN][1000 genomes]
rs1636256	0.85[ASN][1000 genomes]
rs1639034	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1639036	0.97[ASN][1000 genomes]
rs1639040	0.97[ASN][1000 genomes]
rs1639064	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1639065	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1639066	0.94[ASN][1000 genomes]
rs1713913	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1713921	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2527677	0.95[ASN][1000 genomes]
rs2527680	0.94[ASN][1000 genomes]
rs2527681	0.93[ASN][1000 genomes]
rs2533867	0.96[ASN][1000 genomes]
rs2533868	0.96[ASN][1000 genomes]
rs2533870	0.96[ASN][1000 genomes]
rs2533871	0.94[ASN][1000 genomes]
rs2533875	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2533877	0.93[ASN][1000 genomes]
rs2533891	0.94[ASN][1000 genomes]
rs2644281	0.96[ASN][1000 genomes]
rs2644286	0.96[ASN][1000 genomes]
rs2644293	0.94[ASN][1000 genomes]
rs2644300	0.95[ASN][1000 genomes]
rs2644309	0.94[ASN][1000 genomes]
rs2679259	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs71522301	0.95[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	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
7	esv3333602	chr7:2882776-2885274	Enhancers Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1636252	GNA12	cis	Nerve Tibial	GTEx
rs1636252	GNA12	Cis_1M	lymphoblastoid	RTeQTL
rs1636252	GNA12	cis	Artery Tibial	GTEx
rs1636252	GNA12	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:2882400-2885000	Active TSS	A549	lung
2	chr7:2884200-2885000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
3	chr7:2884200-2885000	Active TSS	Primary T killer memory cells from peripheral blood	blood
4	chr7:2884400-2885000	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
5	chr7:2884400-2885000	Flanking Active TSS	Duodenum Mucosa	Duodenum
6	chr7:2884400-2885000	Flanking Active TSS	HepG2	liver
7	chr7:2884400-2885000	Flanking Active TSS	K562	blood
8	chr7:2884600-2885000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr7:2884600-2885000	Enhancers	Primary monocytes fromperipheralblood	blood
10	chr7:2884600-2885000	Enhancers	Placenta	Placenta
11	chr7:2884600-2885000	Enhancers	Fetal Thymus	thymus
12	chr7:2884600-2885000	Enhancers	NHEK	skin
13	chr7:2884600-2885600	Weak transcription	Lung	lung
14	chr7:2884600-2889600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr7:2884600-2889600	Weak transcription	Fetal Kidney	kidney
16	chr7:2884600-2896000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr7:2884600-2902800	Weak transcription	Right Ventricle	heart
18	chr7:2884800-2885000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr7:2884800-2885000	Enhancers	iPS-15b Cell Line	embryonic stem cell
20	chr7:2884800-2885000	Enhancers	iPS-18 Cell Line	embryonic stem cell
21	chr7:2884800-2885000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr7:2884800-2885000	Enhancers	Primary hematopoietic stem cells	blood
23	chr7:2884800-2885000	Enhancers	Primary T helper naive cells from peripheral blood	blood
24	chr7:2884800-2885000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
25	chr7:2884800-2885000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr7:2884800-2885000	Enhancers	Dnd41	blood
27	chr7:2884800-2885000	Enhancers	Monocytes-CD14+_RO01746	blood
28	chr7:2884800-2885400	Enhancers	Fetal Intestine Large	intestine
29	chr7:2884800-2885600	Enhancers	Fetal Intestine Small	intestine
30	chr7:2884800-2886600	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr7:2884800-2887800	Weak transcription	H1 Cell Line	embryonic stem cell
32	chr7:2884800-2887800	Weak transcription	Rectal Mucosa Donor 29	rectum
33	chr7:2884800-2889600	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr7:2884800-2889800	Weak transcription	Fetal Brain Male	brain
35	chr7:2884800-2889800	Weak transcription	Pancreas	Pancrea
36	chr7:2884800-2890600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr7:2884800-2891000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr7:2884800-2891200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr7:2884800-2891200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr7:2884800-2895800	Weak transcription	Fetal Heart	heart

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