Variant report

Variant	rs10992234
Chromosome Location	chr9:94877836-94877837
allele	A/G
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	RELA	chr9:94877147-94878037	GM15510	blood:	n/a	n/a
2	RCOR1	chr9:94877537-94878029	K562	blood:	n/a	n/a
3	YY1	chr9:94877320-94877847	HepG2	liver:	n/a	chr9:94877399-94877413 chr9:94877734-94877748 chr9:94877401-94877410 chr9:94877743-94877754 chr9:94877404-94877413
4	BHLHE40	chr9:94877477-94878106	GM12878	blood:	n/a	n/a
5	TAF1	chr9:94877289-94878003	MCF-7	breast:	n/a	n/a
6	ATF3	chr9:94877525-94877863	HepG2	liver:	n/a	n/a
7	PAX5	chr9:94877430-94877957	GM12878	blood:	n/a	n/a
8	GABPA	chr9:94877017-94877985	MCF-7	breast:	n/a	chr9:94877401-94877410 chr9:94877775-94877784 chr9:94877773-94877787
9	TBP	chr9:94877169-94877968	HepG2	liver:	n/a	n/a
10	CREB1	chr9:94877130-94878106	HepG2	liver:	n/a	n/a
11	GABPA	chr9:94877256-94877986	SK-N-SH	brain:	n/a	chr9:94877401-94877410 chr9:94877775-94877784 chr9:94877773-94877787
12	BCLAF1	chr9:94877439-94878087	GM12878	blood:	n/a	chr9:94877743-94877752 chr9:94877741-94877754 chr9:94877746-94877755
13	YY1	chr9:94877267-94878106	GM12878	blood:	n/a	chr9:94877399-94877413 chr9:94877734-94877748 chr9:94877401-94877410 chr9:94877743-94877754 chr9:94877404-94877413
14	GABPA	chr9:94877477-94877888	Hela-S3	cervix:	n/a	chr9:94877775-94877784 chr9:94877773-94877787
15	POLR2A	chr9:94877334-94878010	H1-hESC	embryonic stem cell:	n/a	n/a
16	POLR2A	chr9:94877417-94877902	A549	lung:	n/a	n/a
17	SRF	chr9:94877333-94878008	HCT-116	colon:	n/a	chr9:94877737-94877747
18	POLR2A	chr9:94877396-94877997	A549	lung:	n/a	n/a
19	TAF1	chr9:94877411-94877928	GM12892	blood:	n/a	n/a
20	MAX	chr9:94877504-94877866	HepG2	liver:	n/a	chr9:94877737-94877747
21	NRF1	chr9:94877571-94878025	GM12878	blood:	n/a	chr9:94877775-94877784 chr9:94877773-94877784 chr9:94877773-94877787
22	FOS	chr9:94877655-94877856	MCF10A-Er-Src	breast:	n/a	chr9:94877741-94877750
23	THAP1	chr9:94877621-94877861	K562	blood:	n/a	n/a
24	GABPA	chr9:94877395-94877904	K562	blood:	n/a	chr9:94877401-94877410 chr9:94877775-94877784 chr9:94877773-94877787
25	ATF3	chr9:94877431-94877938	GM12878	blood:	n/a	n/a
26	USF2	chr9:94877549-94877952	H1-hESC	embryonic stem cell:	n/a	n/a
27	SRF	chr9:94877214-94878134	HCT-116	colon:	n/a	chr9:94877737-94877747
28	ZNF143	chr9:94877529-94877881	H1-hESC	embryonic stem cell:	n/a	n/a
29	ZNF384	chr9:94877517-94878089	GM12878	blood:	n/a	n/a
30	SIN3AK20	chr9:94877354-94877961	PANC-1	pancreas:	n/a	n/a
31	CHD1	chr9:94877463-94877996	GM12878	blood:	n/a	n/a
32	POLR2A	chr9:94877387-94878091	SK-N-SH	brain:	n/a	n/a
33	PML	chr9:94877183-94878035	K562	blood:	n/a	n/a
34	POLR2A	chr9:94877382-94877918	H1-hESC	embryonic stem cell:	n/a	n/a
35	ELK4	chr9:94877420-94877910	Hela-S3	cervix:	n/a	n/a
36	PML	chr9:94877228-94878223	GM12878	blood:	n/a	n/a
37	STAT3	chr9:94877619-94877978	Hela-S3	cervix:	n/a	chr9:94877828-94877842
38	ZEB1	chr9:94877520-94877889	GM12878	blood:	n/a	n/a
39	GTF2B	chr9:94877598-94877949	K562	blood:	n/a	n/a
40	YY1	chr9:94877227-94877935	HepG2	liver:	n/a	chr9:94877399-94877413 chr9:94877734-94877748 chr9:94877401-94877410 chr9:94877743-94877754 chr9:94877404-94877413
41	CCNT2	chr9:94877453-94877920	K562	blood:	n/a	n/a
42	HCFC1	chr9:94877192-94877998	K562	blood:	n/a	n/a
43	POLR2A	chr9:94877320-94878087	GM12892	blood:	n/a	n/a
44	POU2F2	chr9:94877421-94877931	GM12891	blood:	n/a	n/a
45	POLR2A	chr9:94877371-94878102	K562	blood:	n/a	n/a
46	FOXA2	chr9:94877619-94877941	HepG2	liver:	n/a	n/a
47	POLR2A	chr9:94877389-94878047	HepG2	liver:	n/a	n/a
48	SP1	chr9:94877283-94878135	HCT-116	colon:	n/a	chr9:94877737-94877747 chr9:94877399-94877411 chr9:94877736-94877748 chr9:94877400-94877410 chr9:94877737-94877746 chr9:94877400-94877409 chr9:94877401-94877410 chr9:94877738-94877747 chr9:94877736-94877748 chr9:94877399-94877411 chr9:94877733-94877747
49	POLR2A	chr9:94877125-94878717	GM12891	blood:	n/a	n/a
50	FOS	chr9:94877594-94877852	MCF10A-Er-Src	breast:	n/a	chr9:94877741-94877750

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr9:94877805-94877855	SAEC	small airway:	n/a
2	chr9:94877805-94877855	NT2-D1	testis:	n/a
3	chr9:94877805-94877855	HepG2	liver:	n/a
4	chr9:94877805-94877855	HEK293	kidney:	embryo
5	chr9:94877805-94877855	SK-N-SH_RA	brain:	n/a
6	chr9:94877805-94877855	NB4	blood:	n/a
7	chr9:94877805-94877855	A549	lung:	n/a
8	chr9:94877805-94877855	LNCaP	prostate:	n/a
9	chr9:94877805-94877855	PANC-1	pancreas:	n/a
10	chr9:94877805-94877855	T-47D	breast:	n/a
11	chr9:94877805-94877855	AG04449	skin:	fetal
12	chr9:94877805-94877855	AG09319	gingival:	n/a
13	chr9:94877805-94877855	MCF-7	breast:	n/a
14	chr9:94877805-94877855	SK-N-MC	brain:	n/a
15	chr9:94877805-94877855	H1-hESC	embryonic stem cell:	embryo
16	chr9:94877805-94877855	ECC-1	luminal epithelium:	n/a
17	chr9:94877805-94877855	HPAEpiC	pulmonary alveolar:	n/a
18	chr9:94877805-94877855	HCM	heart:	n/a
19	chr9:94877805-94877855	ProgFib	skin:	n/a
20	chr9:94877805-94877855	HNPCEpiC	eye:	n/a
21	chr9:94877805-94877855	CMK	blood:	n/a
22	chr9:94877805-94877855	AG09309	skin:	n/a
23	chr9:94877805-94877855	AG04450	lung:	fetal
24	chr9:94877805-94877855	HRPEpiC	eye:	n/a
25	chr9:94877805-94877855	HRCEpiC	kidney:	n/a
26	chr9:94877805-94877855	HCT-116	colon:	n/a
27	chr9:94877805-94877855	GM12891	blood:	n/a
28	chr9:94877805-94877855	U87	brain:	n/a
29	chr9:94877805-94877855	NHBE	bronchial:	n/a
30	chr9:94877805-94877855	Jurkat	blood:	n/a
31	chr9:94877805-94877855	MCF10A-Er-Src	breast:	n/a
32	chr9:94877805-94877855	PrEC	prostate:	n/a
33	chr9:94877805-94877855	BJ	skin:	n/a
34	chr9:94877805-94877855	GM12892	blood:	n/a
35	chr9:94877805-94877855	IMR90	lung:	fetal
36	chr9:94877805-94877855	ovcar-3	ovarian:	n/a
37	chr9:94877805-94877855	HRE	kidney:	n/a
38	chr9:94877805-94877855	GM12878	blood:	n/a
39	chr9:94877805-94877855	HUVEC	blood vessel:	n/a
40	chr9:94877805-94877855	HIPEpiC	eye:	n/a
41	chr9:94877805-94877855	HL-60	blood:	n/a
42	chr9:94877805-94877855	GM06990	blood:	n/a
43	chr9:94877805-94877855	Hepatocyte	liver:	n/a
44	chr9:94877805-94877855	HMEC	breast:	n/a
45	chr9:94877805-94877855	Hela-S3	cervix:	n/a
46	chr9:94877805-94877855	HCPEpiC	choroid plexus:	n/a
47	chr9:94877805-94877855	AoSMC	blood vessel:	n/a
48	chr9:94877805-94877855	BE2_C	brain:	n/a
49	chr9:94877805-94877855	HAEpiC	amniotic membrane:	n/a
50	chr9:94877805-94877855	NHDF-neo	bronchial:	n/a

No.	Distal block	Cell Line	Cell type
1	chr17:57922613..57925300-chr9:94876383..94878683,2	MCF-7	breast:
2	chr9:94875730..94878651-chr9:95055011..95057658,2	K562	blood:
3	chr9:94859639..94862481-chr9:94877750..94879345,2	MCF-7	breast:
4	chr9:94867851..94872295-chr9:94876110..94878962,5	MCF-7	breast:
5	chr9:94875796..94880000-chr9:95086097..95090720,4	MCF-7	breast:
6	chr9:94876370..94880607-chr9:95003262..95006634,4	MCF-7	breast:
7	chr9:94871412..94875028-chr9:94875797..94879228,6	K562	blood:
8	chr3:129034213..129034773-chr9:94877279..94878170,2	Hela-S3	cervix:
9	chr6:26124264..26124781-chr9:94877459..94878037,2	Hela-S3	cervix:
10	chr9:94871544..94874605-chr9:94874619..94877875,5	MCF-7	breast:
11	chr1:149223711..149225269-chr9:94877286..94878841,2	MCF-7	breast:
12	chr9:94876692..94878485-chr9:95054878..95056695,2	MCF-7	breast:
13	chr12:49525092..49525919-chr9:94877747..94878616,2	HCT-116	colon:

Variant related genes	Relation type
SPTLC1	TF binding region
SPTLC1	CpG island
ENSG00000198000	Chromatin interaction
ENSG00000240791	Chromatin interaction
ENSG00000232179	Chromatin interaction
ENSG00000258017	Chromatin interaction
ENSG00000228069	Chromatin interaction
ENSG00000201524	Chromatin interaction
ENSG00000188312	Chromatin interaction
ENSG00000180573	Chromatin interaction
ENSG00000123416	Chromatin interaction
ENSG00000238288	Chromatin interaction
ENSG00000206737	Chromatin interaction
ENSG00000206417	Chromatin interaction
ENSG00000227321	Chromatin interaction
ENSG00000090054	Chromatin interaction
ENSG00000196305	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10512220	0.81[JPT][hapmap]
rs10739925	0.81[JPT][hapmap]
rs10761143	0.81[JPT][hapmap]
rs10820936	0.81[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.87[TSI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10820937	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10820938	0.82[MEX][hapmap]
rs10992221	1.00[CEU][hapmap];0.95[MEX][hapmap];0.82[YRI][hapmap];0.84[AMR][1000 genomes]
rs1892268	0.81[JPT][hapmap]
rs1970121	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2297568	0.81[JPT][hapmap]
rs28727560	0.99[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2895201	0.81[JPT][hapmap]
rs3750440	0.89[CEU][hapmap];0.80[JPT][hapmap]
rs3847308	0.89[JPT][hapmap]
rs4307406	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58129324	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6479400	0.81[JPT][hapmap]
rs6479403	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7020136	0.81[JPT][hapmap]
rs7024583	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7029539	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7041193	0.81[JPT][hapmap]
rs7046540	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7848874	0.81[JPT][hapmap]
rs7852067	1.00[CEU][hapmap];0.82[YRI][hapmap];0.85[AMR][1000 genomes]
rs7856177	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7858659	0.81[CEU][hapmap];0.91[MEX][hapmap]
rs7860518	0.90[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.87[TSI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7863564	0.82[EUR][1000 genomes]
rs7869504	0.81[JPT][hapmap]
rs7871444	0.81[JPT][hapmap]
rs7872515	1.00[CEU][hapmap];0.95[MEX][hapmap];0.82[YRI][hapmap];0.84[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949008	chr9:94500776-95182133	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv1050845	chr9:94687959-95312406	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
3	nsv1046733	chr9:94690622-95138564	Genic enhancers Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv530947	chr9:94697309-95093377	Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
5	nsv917089	chr9:94857047-95099848	Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10992234	FBP1	cis	parietal	SCAN
rs10992234	SPTLC1	cis	parietal	SCAN
rs10992234	CDK20	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:94875800-94878400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr9:94876000-94878400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr9:94876000-94878600	Active TSS	HUES64 Cell Line	embryonic stem cell
4	chr9:94876000-94878600	Active TSS	Rectal Mucosa Donor 29	rectum
5	chr9:94876200-94878400	Active TSS	Fetal Lung	lung
6	chr9:94876200-94878600	Active TSS	Psoas Muscle	Psoas
7	chr9:94876400-94878200	Active TSS	Duodenum Mucosa	Duodenum
8	chr9:94876400-94878400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr9:94876400-94878400	Active TSS	Esophagus	oesophagus
10	chr9:94876400-94878400	Active TSS	Right Atrium	heart
11	chr9:94876400-94878400	Active TSS	Hela-S3	cervix
12	chr9:94876400-94878400	Active TSS	NHDF-Ad	bronchial
13	chr9:94876400-94878600	Active TSS	iPS-20b Cell Line	embryonic stem cell
14	chr9:94876400-94878600	Active TSS	A549	lung
15	chr9:94876400-94878600	Active TSS	NHLF	lung
16	chr9:94876400-94878800	Active TSS	GM12878-XiMat	blood
17	chr9:94876600-94878200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr9:94876600-94878200	Active TSS	HMEC	breast
19	chr9:94876600-94878200	Active TSS	HSMM	muscle
20	chr9:94876600-94878200	Active TSS	K562	blood
21	chr9:94876600-94878200	Active TSS	NHEK	skin
22	chr9:94876600-94878400	Active TSS	H9 Cell Line	embryonic stem cell
23	chr9:94876600-94878400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr9:94876600-94878400	Active TSS	HUES48 Cell Line	embryonic stem cell
25	chr9:94876600-94878400	Active TSS	iPS-15b Cell Line	embryonic stem cell
26	chr9:94876600-94878400	Active TSS	iPS-18 Cell Line	embryonic stem cell
27	chr9:94876600-94878400	Active TSS	Breast Myoepithelial Primary Cells	Breast
28	chr9:94876600-94878400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr9:94876600-94878400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr9:94876600-94878600	Active TSS	HUES6 Cell Line	embryonic stem cell
31	chr9:94876600-94878600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr9:94876600-94878600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr9:94876600-94878600	Active TSS	Fetal Brain Female	brain
34	chr9:94876800-94878000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr9:94876800-94878000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr9:94876800-94878000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
37	chr9:94876800-94878200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr9:94876800-94878200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr9:94876800-94878200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
40	chr9:94876800-94878200	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
41	chr9:94876800-94878200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr9:94876800-94878200	Active TSS	Muscle Satellite Cultured Cells	--
43	chr9:94876800-94878200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr9:94876800-94878200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr9:94876800-94878200	Active TSS	Colonic Mucosa	Colon
46	chr9:94876800-94878200	Active TSS	Colon Smooth Muscle	Colon
47	chr9:94876800-94878200	Active TSS	Fetal Intestine Small	intestine
48	chr9:94876800-94878200	Active TSS	Gastric	stomach
49	chr9:94876800-94878200	Active TSS	Lung	lung
50	chr9:94876800-94878200	Active TSS	HSMMtube	muscle

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