Variant report

Variant	rs1639040
Chromosome Location	chr7:2884116-2884117
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	GABPA	chr7:2883895-2884244	A549	lung:	n/a	n/a
2	MAX	chr7:2883501-2884512	K562	blood:	n/a	chr7:2883882-2883891
3	TAF1	chr7:2883429-2884130	HepG2	liver:	n/a	n/a
4	ATF1	chr7:2883937-2884453	K562	blood:	n/a	n/a
5	SP2	chr7:2883889-2884516	HepG2	liver:	n/a	chr7:2884188-2884203 chr7:2884114-2884129 chr7:2884051-2884061
6	ELK1	chr7:2883950-2884493	GM12878	blood:	n/a	n/a
7	GABPA	chr7:2883967-2884222	A549	lung:	n/a	n/a
8	POLR2A	chr7:2883500-2884583	GM18505	blood:	n/a	n/a
9	SP2	chr7:2883919-2884453	H1-hESC	embryonic stem cell:	n/a	chr7:2884188-2884203 chr7:2884114-2884129 chr7:2884051-2884061
10	CEBPB	chr7:2883965-2884393	Hela-S3	cervix:	n/a	chr7:2884053-2884061
11	YY1	chr7:2883805-2884489	SK-N-SH_RA	brain:	n/a	chr7:2883916-2883925 chr7:2883916-2883927 chr7:2883908-2883922
12	SP2	chr7:2883947-2884470	H1-hESC	embryonic stem cell:	n/a	chr7:2884188-2884203 chr7:2884114-2884129 chr7:2884051-2884061
13	RFX5	chr7:2883976-2884652	GM12878	blood:	n/a	n/a
14	FOS	chr7:2883872-2884437	GM12878	blood:	n/a	chr7:2884192-2884201 chr7:2884073-2884082
15	ELF1	chr7:2883690-2884377	GM12878	blood:	n/a	chr7:2883916-2883925 chr7:2883915-2883927 chr7:2883918-2883930
16	PBX3	chr7:2883836-2884318	A549	lung:	n/a	n/a
17	POLR2A	chr7:2883903-2884862	PANC-1	pancreas:	n/a	n/a
18	POLR2A	chr7:2883918-2884574	GM12878	blood:	n/a	n/a
19	HCFC1	chr7:2883693-2884614	Hela-S3	cervix:	n/a	n/a
20	ELF1	chr7:2883835-2884473	MCF-7	breast:	n/a	chr7:2883916-2883925 chr7:2883915-2883927 chr7:2883918-2883930
21	SP1	chr7:2883832-2884578	H1-hESC	embryonic stem cell:	n/a	chr7:2884192-2884204 chr7:2884193-2884202 chr7:2884206-2884220 chr7:2884488-2884502 chr7:2884098-2884107 chr7:2884097-2884109 chr7:2884192-2884204 chr7:2884193-2884203 chr7:2884209-2884220 chr7:2884209-2884221 chr7:2884099-2884108 chr7:2884098-2884108 chr7:2884099-2884108 chr7:2884097-2884109 chr7:2884194-2884203 chr7:2883884-2883894 chr7:2884192-2884203
22	THAP1	chr7:2883546-2884293	K562	blood:	n/a	n/a
23	GABPA	chr7:2883812-2884172	HepG2	liver:	n/a	n/a
24	SP1	chr7:2883890-2884689	A549	lung:	n/a	chr7:2884192-2884204 chr7:2884193-2884202 chr7:2884206-2884220 chr7:2884488-2884502 chr7:2884098-2884107 chr7:2884097-2884109 chr7:2884192-2884204 chr7:2884193-2884203 chr7:2884209-2884220 chr7:2884209-2884221 chr7:2884099-2884108 chr7:2884098-2884108 chr7:2884099-2884108 chr7:2884097-2884109 chr7:2884194-2884203 chr7:2884192-2884203
25	FOXP2	chr7:2883725-2884351	PFSK-1	brain:	n/a	n/a
26	CREB1	chr7:2883559-2884479	A549	lung:	n/a	n/a
27	POLR2A	chr7:2883759-2884691	GM12878	blood:	n/a	n/a
28	BHLHE40	chr7:2883930-2884522	HepG2	liver:	n/a	n/a
29	POLR2A	chr7:2883429-2884614	MCF-7	breast:	n/a	n/a
30	STAT1	chr7:2883927-2884349	GM12878	blood:	n/a	n/a
31	ZNF143	chr7:2884038-2884808	K562	blood:	n/a	n/a
32	IRF1	chr7:2883870-2884701	K562	blood:	n/a	chr7:2884192-2884206
33	EBF1	chr7:2884027-2884511	GM12878	blood:	n/a	n/a
34	NFYA	chr7:2883831-2884507	K562	blood:	n/a	chr7:2884147-2884161 chr7:2884053-2884065 chr7:2884049-2884064 chr7:2884049-2884064 chr7:2884045-2884063 chr7:2884050-2884064
35	GABPA	chr7:2883942-2884189	GM12878	blood:	n/a	n/a
36	POLR2A	chr7:2883556-2884563	MCF10A-Er-Src	breast:	n/a	n/a
37	CREB1	chr7:2883847-2884490	H1-hESC	embryonic stem cell:	n/a	n/a
38	RFX5	chr7:2882892-2885962	SK-N-SH	brain:	n/a	n/a
39	USF1	chr7:2883849-2884147	SK-N-SH_RA	brain:	n/a	chr7:2883924-2883940 chr7:2883916-2883932 chr7:2883907-2883923
40	CEBPZ	chr7:2883967-2884577	HepG2	liver:	n/a	n/a
41	POLR2A	chr7:2883127-2884546	H1-neurons	neurons:	n/a	n/a
42	MAX	chr7:2883537-2884367	Hela-S3	cervix:	n/a	chr7:2883882-2883891
43	POLR2A	chr7:2883595-2884554	HepG2	liver:	n/a	n/a
44	MAZ	chr7:2883431-2884657	K562	blood:	n/a	chr7:2883882-2883891 chr7:2883465-2883475
45	POLR2A	chr7:2883622-2884578	NB4	blood:	n/a	n/a
46	POLR2A	chr7:2883354-2884645	GM12892	blood:	n/a	n/a
47	BRCA1	chr7:2884017-2884306	Hela-S3	cervix:	n/a	n/a
48	CHD2	chr7:2883877-2884544	K562	blood:	n/a	n/a
49	MAFK	chr7:2883991-2884693	Hela-S3	cervix:	n/a	chr7:2884563-2884579 chr7:2884561-2884572 chr7:2884407-2884418 chr7:2884560-2884575 chr7:2884561-2884581
50	CREB1	chr7:2883826-2884632	K562	blood:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr7:2884079-2884129	HepG2	liver:	n/a
2	chr7:2884079-2884129	BE2_C	brain:	n/a
3	chr7:2884079-2884129	HRCEpiC	kidney:	n/a
4	chr7:2884079-2884129	GM06990	blood:	n/a
5	chr7:2884079-2884129	ECC-1	luminal epithelium:	n/a
6	chr7:2884079-2884129	HNPCEpiC	eye:	n/a
7	chr7:2884079-2884129	AG09309	skin:	n/a
8	chr7:2884079-2884129	CMK	blood:	n/a
9	chr7:2884079-2884129	PrEC	prostate:	n/a
10	chr7:2884079-2884129	AG04449	skin:	fetal
11	chr7:2884079-2884129	AoSMC	blood vessel:	n/a
12	chr7:2884079-2884129	HEEpiC	esophagus:	n/a
13	chr7:2884079-2884129	Jurkat	blood:	n/a
14	chr7:2884079-2884129	NT2-D1	testis:	n/a
15	chr7:2884079-2884129	NHBE	bronchial:	n/a
16	chr7:2884079-2884129	HEK293	kidney:	embryo
17	chr7:2884079-2884129	Caco-2	colon:	n/a
18	chr7:2884079-2884129	SKMC	muscle:	n/a
19	chr7:2884079-2884129	T-47D	breast:	n/a
20	chr7:2884079-2884129	Hepatocyte	liver:	n/a
21	chr7:2884079-2884129	GM12891	blood:	n/a
22	chr7:2884079-2884129	AG09319	gingival:	n/a
23	chr7:2884079-2884129	SK-N-MC	brain:	n/a
24	chr7:2884079-2884129	Hela-S3	cervix:	n/a
25	chr7:2884079-2884129	HL-60	blood:	n/a
26	chr7:2884079-2884129	HMEC	breast:	n/a
27	chr7:2884079-2884129	PFSK-1	brain:	n/a
28	chr7:2884079-2884129	MCF-7	breast:	n/a
29	chr7:2884079-2884129	ProgFib	skin:	n/a
30	chr7:2884079-2884129	K562	blood:	n/a
31	chr7:2884079-2884129	HPAEpiC	pulmonary alveolar:	n/a
32	chr7:2884079-2884129	RPTEC	kidney:	n/a
33	chr7:2884079-2884129	BJ	skin:	n/a
34	chr7:2884079-2884129	SK-N-SH_RA	brain:	n/a
35	chr7:2884079-2884129	AG04450	lung:	fetal
36	chr7:2884079-2884129	HCF	heart:	n/a
37	chr7:2884079-2884129	HCM	heart:	n/a
38	chr7:2884079-2884129	HUVEC	blood vessel:	n/a
39	chr7:2884079-2884129	HAEpiC	amniotic membrane:	n/a
40	chr7:2884079-2884129	PANC-1	pancreas:	n/a
41	chr7:2884079-2884129	HIPEpiC	eye:	n/a
42	chr7:2884079-2884129	GM12892	blood:	n/a
43	chr7:2884079-2884129	GM12878	blood:	n/a
44	chr7:2884079-2884129	NH-A	brain:	n/a
45	chr7:2884079-2884129	LNCaP	prostate:	n/a
46	chr7:2884079-2884129	NB4	blood:	n/a
47	chr7:2884079-2884129	HRE	kidney:	n/a
48	chr7:2884079-2884129	ovcar-3	ovarian:	n/a
49	chr7:2884079-2884129	HRPEpiC	eye:	n/a
50	chr7:2884079-2884129	U87	brain:	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:149858014..149859677-chr7:2882924..2885730,2	MCF-7	breast:
2	chr7:2869377..2877481-chr7:2880306..2885399,15	MCF-7	breast:
3	chr7:2801788..2804432-chr7:2882018..2884117,3	K562	blood:
4	chr7:2726313..2732670-chr7:2878755..2886203,10	MCF-7	breast:

Variant related genes	Relation type
GNA12	TF binding region
GNA12	CpG island
ENSG00000184270	Chromatin interaction
ENSG00000174945	Chromatin interaction
ENSG00000184678	Chromatin interaction
ENSG00000178096	Chromatin interaction
ENSG00000184260	Chromatin interaction
ENSG00000146535	Chromatin interaction
ENSG00000231357	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs1182155	0.86[EUR][1000 genomes]
rs1182199	0.82[EUR][1000 genomes]
rs11973498	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12700373	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13230946	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13230995	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1614791	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1636247	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1636248	0.92[ASN][1000 genomes]
rs1636249	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1636250	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1636251	0.95[ASN][1000 genomes]
rs1636252	0.97[ASN][1000 genomes]
rs1636253	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1636254	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1636255	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1636256	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1636264	0.82[EUR][1000 genomes]
rs1639034	0.96[ASN][1000 genomes]
rs1639036	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1639066	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1713912	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1713921	0.93[ASN][1000 genomes]
rs2527677	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2527680	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2527681	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2533867	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2533868	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2533870	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2533871	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2533875	0.94[ASN][1000 genomes]
rs2533877	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2533878	0.81[EUR][1000 genomes]
rs2533889	0.82[EUR][1000 genomes]
rs2533891	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2644281	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2644286	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2644293	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2644300	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2644309	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2679259	0.96[ASN][1000 genomes]
rs71522301	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs71522302	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs71524003	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7783400	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[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
rs1639040	GNA12	cis	Nerve Tibial	GTEx
rs1639040	GNA12	cis	multi-tissue	Pritchard
rs1639040	GNA12	cis	Artery Tibial	GTEx
rs1639040	GNA12	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:2882000-2884400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr7:2882000-2884600	Active TSS	Pancreatic Islets	Pancreatic Islet
3	chr7:2882400-2884400	Active TSS	HUES48 Cell Line	embryonic stem cell
4	chr7:2882400-2884400	Active TSS	iPS-15b Cell Line	embryonic stem cell
5	chr7:2882400-2884800	Active TSS	NHLF	lung
6	chr7:2882400-2885000	Active TSS	A549	lung
7	chr7:2882600-2884400	Active TSS	ES-I3 Cell Line	embryonic stem cell
8	chr7:2882600-2884400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr7:2882600-2884400	Active TSS	HUES6 Cell Line	embryonic stem cell
10	chr7:2882600-2884400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr7:2882600-2884400	Active TSS	HSMMtube	muscle
12	chr7:2882600-2884600	Active TSS	HUES64 Cell Line	embryonic stem cell
13	chr7:2882600-2884600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr7:2882600-2884800	Active TSS	HSMM	muscle
15	chr7:2882800-2884400	Active TSS	iPS-20b Cell Line	embryonic stem cell
16	chr7:2882800-2884800	Active TSS	H9 Cell Line	embryonic stem cell
17	chr7:2883000-2884400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr7:2883000-2884400	Active TSS	iPS-18 Cell Line	embryonic stem cell
19	chr7:2883000-2884400	Active TSS	Muscle Satellite Cultured Cells	--
20	chr7:2883000-2884400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr7:2883000-2884400	Active TSS	Brain Substantia Nigra	brain
22	chr7:2883000-2884400	Active TSS	Fetal Kidney	kidney
23	chr7:2883000-2884400	Active TSS	Psoas Muscle	Psoas
24	chr7:2883000-2884600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
25	chr7:2883000-2884600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr7:2883000-2884600	Active TSS	NHDF-Ad	bronchial
27	chr7:2883000-2884800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr7:2883000-2884800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr7:2883200-2884200	Active TSS	HUVEC	blood vessel
30	chr7:2883200-2884400	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr7:2883200-2884400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr7:2883200-2884400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr7:2883200-2884400	Active TSS	Breast Myoepithelial Primary Cells	Breast
34	chr7:2883200-2884400	Active TSS	Primary T cells from cord blood	blood
35	chr7:2883200-2884400	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
36	chr7:2883200-2884400	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr7:2883200-2884400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr7:2883200-2884400	Active TSS	Brain Anterior Caudate	brain
39	chr7:2883200-2884400	Active TSS	Duodenum Mucosa	Duodenum
40	chr7:2883200-2884400	Active TSS	Fetal Brain Female	brain
41	chr7:2883200-2884400	Active TSS	Fetal Intestine Large	intestine
42	chr7:2883200-2884400	Active TSS	Fetal Lung	lung
43	chr7:2883200-2884400	Active TSS	Right Ventricle	heart
44	chr7:2883200-2884400	Active TSS	GM12878-XiMat	blood
45	chr7:2883200-2884400	Active TSS	HepG2	liver
46	chr7:2883200-2884400	Active TSS	HMEC	breast
47	chr7:2883200-2884400	Active TSS	NH-A	brain
48	chr7:2883200-2884400	Active TSS	NHEK	skin
49	chr7:2883200-2884600	Active TSS	H1 Cell Line	embryonic stem cell
50	chr7:2883200-2884600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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