Variant report

Variant	rs7517044
Chromosome Location	chr1:92198162-92198163
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	FOS	chr1:92198080-92198409	MCF10A-Er-Src	breast:	n/a	chr1:92198242-92198252 chr1:92198242-92198252 chr1:92198241-92198253 chr1:92198242-92198252 chr1:92198244-92198255 chr1:92198242-92198251
2	GATA2	chr1:92197803-92198422	K562	blood:	n/a	chr1:92198244-92198253
3	USF1	chr1:92197897-92198561	ECC-1	luminal epithelium:	n/a	n/a
4	MTA3	chr1:92197327-92198423	GM12878	blood:	n/a	n/a
5	TCF7L2	chr1:92197343-92198456	PANC-1	pancreas:	n/a	chr1:92198242-92198251
6	STAT1	chr1:92197822-92198462	K562	blood:	n/a	chr1:92198106-92198126 chr1:92198112-92198120 chr1:92198106-92198126 chr1:92198110-92198121 chr1:92198109-92198123 chr1:92198242-92198251
7	RUNX3	chr1:92197296-92198408	GM12878	blood:	n/a	chr1:92197576-92197585 chr1:92197576-92197585
8	MAFK	chr1:92197685-92198451	K562	blood:	n/a	n/a
9	YY1	chr1:92198111-92198400	HCT-116	colon:	n/a	n/a
10	PAX5	chr1:92197867-92198448	GM12878	blood:	n/a	chr1:92198175-92198193
11	FOSL1	chr1:92198016-92198437	K562	blood:	n/a	chr1:92198242-92198252 chr1:92198242-92198252 chr1:92198241-92198252 chr1:92198241-92198253 chr1:92198242-92198252 chr1:92198244-92198255 chr1:92198242-92198251
12	MAX	chr1:92197926-92198551	A549	lung:	n/a	n/a
13	SMC3	chr1:92197395-92198452	Hela-S3	cervix:	n/a	chr1:92198258-92198265
14	TEAD4	chr1:92197768-92198867	K562	blood:	n/a	n/a
15	MAX	chr1:92198035-92198481	A549	lung:	n/a	n/a
16	CHD2	chr1:92197960-92198520	K562	blood:	n/a	n/a
17	HCFC1	chr1:92197885-92198458	K562	blood:	n/a	n/a
18	ARID3A	chr1:92197761-92198425	K562	blood:	n/a	n/a
19	POLR2A	chr1:92194683-92199275	HepG2	liver:	n/a	n/a
20	MYC	chr1:92197912-92198454	Hela-S3	cervix:	n/a	n/a
21	TEAD4	chr1:92197799-92198556	K562	blood:	n/a	n/a
22	ESR1	chr1:92198011-92198476	ECC-1	luminal epithelium:	n/a	n/a
23	RELA	chr1:92196977-92198384	GM19193	blood:	n/a	chr1:92197588-92197597 chr1:92197586-92197595 chr1:92197588-92197597 chr1:92197586-92197595
24	ZKSCAN1	chr1:92197952-92198491	Hela-S3	cervix:	n/a	n/a
25	JUN	chr1:92197991-92198487	Hela-S3	cervix:	n/a	chr1:92198242-92198252 chr1:92198242-92198252 chr1:92198241-92198253 chr1:92198242-92198252 chr1:92198244-92198255 chr1:92198242-92198251
26	CEBPD	chr1:92197853-92198443	K562	blood:	n/a	n/a
27	MAFF	chr1:92197955-92198407	K562	blood:	n/a	n/a
28	STAT3	chr1:92197412-92198356	MCF10A-Er-Src	breast:	n/a	chr1:92198106-92198126 chr1:92197569-92197580 chr1:92198112-92198120 chr1:92198106-92198126 chr1:92198109-92198123 chr1:92197619-92197631 chr1:92198242-92198251
29	GTF2F1	chr1:92197914-92198465	Hela-S3	cervix:	n/a	n/a
30	TAL1	chr1:92197751-92198519	K562	blood:	n/a	chr1:92198149-92198167
31	NR3C1	chr1:92197966-92198459	ECC-1	luminal epithelium:	n/a	chr1:92198450-92198459
32	RAD21	chr1:92197936-92198370	K562	blood:	n/a	n/a
33	GTF2B	chr1:92197902-92198539	K562	blood:	n/a	n/a
34	TBL1XR1	chr1:92196931-92198817	K562	blood:	n/a	n/a
35	ZMIZ1	chr1:92197873-92198439	K562	blood:	n/a	n/a
36	JUND	chr1:92198092-92198380	HepG2	liver:	n/a	chr1:92198242-92198252 chr1:92198242-92198252 chr1:92198241-92198252 chr1:92198241-92198253 chr1:92198242-92198252 chr1:92198244-92198255 chr1:92198242-92198251
37	MAX	chr1:92197837-92198502	K562	blood:	n/a	n/a
38	STAT5A	chr1:92197791-92198499	K562	blood:	n/a	chr1:92198106-92198126 chr1:92198112-92198120 chr1:92198106-92198126 chr1:92198109-92198123 chr1:92198242-92198251
39	RELA	chr1:92196892-92198345	GM12891	blood:	n/a	chr1:92197588-92197597 chr1:92197586-92197595 chr1:92197588-92197597 chr1:92197586-92197595
40	JUND	chr1:92198142-92198314	H1-hESC	embryonic stem cell:	n/a	chr1:92198242-92198252 chr1:92198242-92198252 chr1:92198241-92198252 chr1:92198241-92198253 chr1:92198242-92198252 chr1:92198244-92198255 chr1:92198242-92198251
41	JUN	chr1:92197964-92198648	K562	blood:	n/a	chr1:92198242-92198252 chr1:92198242-92198252 chr1:92198241-92198253 chr1:92198242-92198252 chr1:92198244-92198255 chr1:92198242-92198251
42	POLR2A	chr1:92197555-92198822	K562	blood:	n/a	n/a
43	ZNF143	chr1:92197978-92198504	K562	blood:	n/a	chr1:92198109-92198127
44	CEBPB	chr1:92197909-92198441	K562	blood:	n/a	n/a
45	SPI1	chr1:92197960-92198337	K562	blood:	n/a	n/a
46	FOSL2	chr1:92198116-92198416	A549	lung:	n/a	chr1:92198242-92198252 chr1:92198242-92198252 chr1:92198241-92198253 chr1:92198242-92198252 chr1:92198244-92198255 chr1:92198242-92198251
47	ESR1	chr1:92197999-92198554	ECC-1	luminal epithelium:	n/a	n/a
48	SMARCC1	chr1:92197492-92198470	Hela-S3	cervix:	n/a	chr1:92198242-92198251
49	FOS	chr1:92198044-92198424	MCF10A-Er-Src	breast:	n/a	chr1:92198242-92198252 chr1:92198242-92198252 chr1:92198241-92198253 chr1:92198242-92198252 chr1:92198244-92198255 chr1:92198242-92198251
50	E2F6	chr1:92197909-92198441	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:92192178..92194320-chr1:92196821..92198679,2	K562	blood:
2	chr1:92195746..92200158-chr1:92212228..92214643,4	K562	blood:
3	chr1:92196121..92198991-chr1:92207192..92209304,2	MCF-7	breast:
4	chr1:92196960..92199922-chr1:92201744..92205146,4	K562	blood:
5	chr1:92186351..92189237-chr1:92195630..92198229,2	K562	blood:
6	chr1:92198152..92200213-chr1:92201193..92206399,7	K562	blood:
7	chr1:92196725..92200248-chr1:92206849..92210560,4	K562	blood:
8	chr1:92197642..92200532-chr1:92350997..92352784,2	K562	blood:
9	chr1:92196718..92198594-chr1:92235219..92237131,2	K562	blood:
10	chr1:92194536..92198402-chr1:92243329..92245903,3	K562	blood:
11	chr1:92197202..92203288-chr1:92206365..92210533,5	K562	blood:

Variant related genes	Relation type
TGFBR3	TF binding region
ENSG00000069702	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10783003	0.82[CHB][hapmap];0.81[ASN][1000 genomes]
rs10783004	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11165354	0.82[CHB][hapmap];0.80[ASN][1000 genomes]
rs11165372	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11165376	0.94[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11165380	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11578802	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12069138	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12069176	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12073224	0.86[CHB][hapmap];0.80[CHD][hapmap]
rs12074859	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12124904	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2087299	0.91[CHB][hapmap];0.84[CHD][hapmap]
rs2306887	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];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4658264	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6604051	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7512284	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009560	chr1:91897078-92270781	Enhancers Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats 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	14 gene(s)	inside rSNPs	diseases
2	nsv1012864	chr1:92067100-92827761	Flanking Active TSS Strong transcription Enhancers Active TSS Weak transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
3	nsv535029	chr1:92067100-92827761	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	esv2763581	chr1:92068967-92203803	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
5	nsv1014990	chr1:92084142-92206674	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
6	nsv530438	chr1:92091957-92827760	Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
7	nsv1010179	chr1:92140209-92655952	Weak transcription Genic enhancers Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
8	nsv535030	chr1:92140209-92655952	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
9	nsv1005917	chr1:92189945-92378683	Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	nsv528991	chr1:92191534-92198162	Weak transcription Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7517044	ARHGAP29	cis	parietal	SCAN
rs7517044	TGFBR3	cis	cerebellum	SCAN

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:92173200-92202400	Weak transcription	Brain Cingulate Gyrus	brain
2	chr1:92189200-92202200	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr1:92190600-92201400	Genic enhancers	NHDF-Ad	bronchial
4	chr1:92191400-92198400	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr1:92191800-92204000	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr1:92192600-92200600	Genic enhancers	Fetal Muscle Leg	muscle
7	chr1:92193000-92202400	Weak transcription	Aorta	Aorta
8	chr1:92193600-92200600	Strong transcription	HepG2	liver
9	chr1:92194400-92201000	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
10	chr1:92194600-92198800	Genic enhancers	Fetal Lung	lung
11	chr1:92195000-92199400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
12	chr1:92195000-92199400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
13	chr1:92195200-92198200	Enhancers	Primary T helper cells PMA-I stimulated	--
14	chr1:92195200-92198400	Enhancers	Right Ventricle	heart
15	chr1:92195400-92198400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
16	chr1:92195400-92198600	Enhancers	Primary T helper cells fromperipheralblood	blood
17	chr1:92195400-92198800	Enhancers	Primary T helper naive cells from peripheral blood	blood
18	chr1:92195600-92198400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
19	chr1:92195600-92198600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr1:92195600-92199200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
21	chr1:92195600-92199200	Enhancers	Fetal Thymus	thymus
22	chr1:92195800-92199400	Genic enhancers	Fetal Stomach	stomach
23	chr1:92196000-92201200	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
24	chr1:92196200-92198200	Enhancers	Liver	Liver
25	chr1:92196200-92198200	Enhancers	Fetal Heart	heart
26	chr1:92196200-92198400	Enhancers	HSMM	muscle
27	chr1:92196200-92198400	Enhancers	NHEK	skin
28	chr1:92196200-92198800	Enhancers	Muscle Satellite Cultured Cells	--
29	chr1:92196200-92198800	Enhancers	Duodenum Smooth Muscle	Duodenum
30	chr1:92196200-92199000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr1:92196200-92199000	Enhancers	Colon Smooth Muscle	Colon
32	chr1:92196200-92199200	Genic enhancers	NHLF	lung
33	chr1:92196400-92198200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr1:92196400-92198200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr1:92196400-92198400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr1:92196400-92198400	Enhancers	Left Ventricle	heart
37	chr1:92196400-92198400	Enhancers	Right Atrium	heart
38	chr1:92196400-92198400	Enhancers	HMEC	breast
39	chr1:92196400-92198600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr1:92196400-92198600	Enhancers	Skeletal Muscle Female	skeletal muscle
41	chr1:92196400-92198800	Enhancers	NH-A	brain
42	chr1:92196400-92200200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr1:92196600-92198200	Enhancers	iPS-18 Cell Line	embryonic stem cell
44	chr1:92196600-92198200	Enhancers	Stomach Mucosa	stomach
45	chr1:92196600-92198400	Enhancers	HUES64 Cell Line	embryonic stem cell
46	chr1:92196600-92198400	Enhancers	Duodenum Mucosa	Duodenum
47	chr1:92196600-92198600	Enhancers	HUES6 Cell Line	embryonic stem cell
48	chr1:92196600-92198800	Enhancers	HSMMtube	muscle
49	chr1:92196600-92199000	Enhancers	Lung	lung
50	chr1:92196600-92199400	Enhancers	Rectal Smooth Muscle	rectum

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