Variant report

Variant	rs1743964
Chromosome Location	chr6:134496112-134496113
allele	C/T
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	NFIC	chr6:134495693-134497117	ECC-1	luminal epithelium:	n/a	n/a
2	GTF2F1	chr6:134495785-134496375	H1-hESC	embryonic stem cell:	n/a	n/a
3	JUND	chr6:134495728-134496501	A549	lung:	n/a	n/a
4	EGR1	chr6:134495767-134496652	HCT-116	colon:	n/a	chr6:134496041-134496054 chr6:134496046-134496056 chr6:134496280-134496290 chr6:134496041-134496054 chr6:134496042-134496056 chr6:134496043-134496053 chr6:134496037-134496059 chr6:134496041-134496054 chr6:134496041-134496054 chr6:134496044-134496053 chr6:134496044-134496054 chr6:134496184-134496197 chr6:134496041-134496055
5	CREB1	chr6:134495712-134496519	A549	lung:	n/a	n/a
6	HA-E2F1	chr6:134495601-134497030	MCF-7	breast:	n/a	chr6:134496568-134496580 chr6:134496050-134496060 chr6:134496046-134496055 chr6:134496659-134496669 chr6:134496572-134496582 chr6:134496665-134496675
7	RAD21	chr6:134495055-134496161	GM12878	blood:	n/a	chr6:134496142-134496156
8	HDAC2	chr6:134495781-134497012	MCF-7	breast:	n/a	chr6:134496537-134496546 chr6:134496012-134496021
9	BRCA1	chr6:134495654-134496131	HepG2	liver:	n/a	n/a
10	POLR2A	chr6:134495542-134497010	MCF-7	breast:	n/a	n/a
11	EP300	chr6:134495768-134496390	SK-N-SH_RA	brain:	n/a	chr6:134496274-134496290
12	JUN	chr6:134495972-134496232	H1-hESC	embryonic stem cell:	n/a	n/a
13	YY1	chr6:134495670-134496339	GM12878	blood:	n/a	chr6:134496041-134496055 chr6:134496009-134496023 chr6:134496180-134496194 chr6:134496186-134496195 chr6:134496046-134496055 chr6:134496278-134496292
14	POLR2A	chr6:134485508-134498148	IMR90	lung:	n/a	n/a
15	POLR2A	chr6:134486381-134497370	MCF10A-Er-Src	breast:	n/a	n/a
16	POLR2A	chr6:134495638-134496466	GM12892	blood:	n/a	n/a
17	REST	chr6:134495805-134496353	SK-N-SH	brain:	n/a	n/a
18	JUN	chr6:134495896-134496410	K562	blood:	n/a	n/a
19	GATA2	chr6:134496017-134496597	K562	blood:	n/a	n/a
20	STAT3	chr6:134496030-134496166	MCF10A-Er-Src	breast:	n/a	n/a
21	TAF1	chr6:134495718-134496229	MCF-7	breast:	n/a	n/a
22	YY1	chr6:134495711-134496998	HepG2	liver:	n/a	chr6:134496041-134496055 chr6:134496652-134496666 chr6:134496661-134496675 chr6:134496009-134496023 chr6:134496667-134496676 chr6:134496180-134496194 chr6:134496186-134496195 chr6:134496046-134496055 chr6:134496278-134496292
23	IRF1	chr6:134495172-134496422	K562	blood:	n/a	chr6:134496045-134496059
24	MAX	chr6:134495819-134496536	K562	blood:	n/a	chr6:134496281-134496291
25	HMGN3	chr6:134495870-134496960	K562	blood:	n/a	chr6:134496871-134496880
26	REST	chr6:134494998-134497181	H1-neurons	neurons:	n/a	n/a
27	CREB1	chr6:134495663-134496302	H1-hESC	embryonic stem cell:	n/a	n/a
28	ZNF143	chr6:134495775-134496434	GM12878	blood:	n/a	chr6:134496274-134496284
29	BHLHE40	chr6:134495937-134496317	GM12878	blood:	n/a	chr6:134496001-134496017 chr6:134496039-134496055
30	MBD4	chr6:134495005-134496282	HepG2	liver:	n/a	n/a
31	POLR2A	chr6:134495794-134496490	HepG2	liver:	n/a	n/a
32	POLR2A	chr6:134495587-134497000	GM12892	blood:	n/a	n/a
33	MAX	chr6:134495810-134496273	HepG2	liver:	n/a	n/a
34	POLR2A	chr6:134493576-134497462	MCF10A-Er-Src	breast:	n/a	n/a
35	POLR2A	chr6:134495716-134496884	GM12878	blood:	n/a	n/a
36	SMC3	chr6:134494757-134496435	GM12878	blood:	n/a	chr6:134496274-134496288
37	BRCA1	chr6:134494783-134496375	Hela-S3	cervix:	n/a	n/a
38	POLR2A	chr6:134495771-134496316	HCT-116	colon:	n/a	n/a
39	KAT2A	chr6:134494989-134496456	Hela-S3	cervix:	n/a	n/a
40	NFIC	chr6:134495642-134496488	HepG2	liver:	n/a	n/a
41	POLR2A	chr6:134495665-134496973	GM18951	blood:	n/a	n/a
42	TCF12	chr6:134495728-134496332	A549	lung:	n/a	n/a
43	POLR2A	chr6:134495756-134496408	HepG2	liver:	n/a	n/a
44	POLR2A	chr6:134495764-134496774	GM10847	blood:	n/a	n/a
45	GATA2	chr6:134495595-134496729	SH-SY5Y	brain:	n/a	chr6:134496646-134496654
46	RELA	chr6:134495100-134496269	GM19193	blood:	n/a	n/a
47	POLR2A	chr6:134495758-134496406	GM18526	blood:	n/a	n/a
48	TCF12	chr6:134495740-134497104	ECC-1	luminal epithelium:	n/a	n/a
49	SP1	chr6:134495105-134496477	A549	lung:	n/a	chr6:134496046-134496056 chr6:134496046-134496056 chr6:134496045-134496057 chr6:134496047-134496056 chr6:134496045-134496057 chr6:134496047-134496056 chr6:134496046-134496055
50	E2F6	chr6:134495718-134496845	A549	lung:	n/a	chr6:134496568-134496580 chr6:134496050-134496060 chr6:134496046-134496055 chr6:134496659-134496669 chr6:134496572-134496582 chr6:134496665-134496675

No.	Distal block	Cell Line	Cell type
1	chr17:20946073..20947073-chr6:134495513..134496122,2	Hela-S3	cervix:
2	chr6:134495483..134497640-chr6:134956428..134958262,2	MCF-7	breast:
3	chr6:30710532..30712736-chr6:134495536..134497342,2	MCF-7	breast:
4	chr17:8339133..8339930-chr6:134495510..134496178,2	Hela-S3	cervix:
5	chr3:57582630..57583369-chr6:134495386..134496237,3	Hela-S3	cervix:
6	chr12:4429962..4430736-chr6:134495433..134496180,2	Hela-S3	cervix:
7	chr15:31283135..31283746-chr6:134495837..134496431,2	Hela-S3	cervix:
8	chr12:72056704..72057665-chr6:134495555..134496174,2	Hela-S3	cervix:
9	chr11:62622868..62623501-chr6:134495305..134496296,2	Hela-S3	cervix:
10	chr17:8059361..8060237-chr6:134495698..134496304,2	Hela-S3	cervix:
11	chr6:134490762..134493490-chr6:134493803..134496901,6	MCF-7	breast:
12	chr1:144533750..144534587-chr6:134495945..134496542,2	Hela-S3	cervix:
13	chr19:12902000..12902515-chr6:134495608..134496584,2	Hela-S3	cervix:
14	chr19:50886596..50888207-chr6:134495627..134497451,2	MCF-7	breast:
15	chr6:134495224..134497350-chr6:134568529..134571029,2	K562	blood:
16	chr6:134493834..134499692-chr6:134846848..134856264,17	MCF-7	breast:
17	chr6:134494166..134496840-chr6:135818948..135820585,2	K562	blood:
18	chr6:134493434..134498023-chr6:134954085..134958006,4	K562	blood:
19	chr1:145382267..145382936-chr6:134495932..134496686,2	Hela-S3	cervix:
20	chr6:134494551..134497365-chr6:135218246..135220036,2	K562	blood:
21	chr6:134495880..134498282-chr6:134775356..134777682,2	MCF-7	breast:

Variant related genes	Relation type
SGK1	TF binding region
ENSG00000133858	Chromatin interaction
ENSG00000118515	Chromatin interaction
ENSG00000124422	Chromatin interaction
ENSG00000231971	Chromatin interaction
ENSG00000137331	Chromatin interaction
ENSG00000168374	Chromatin interaction
ENSG00000166912	Chromatin interaction
ENSG00000231028	Chromatin interaction
ENSG00000213117	Chromatin interaction
ENSG00000201558	Chromatin interaction
ENSG00000179094	Chromatin interaction
ENSG00000171223	Chromatin interaction
ENSG00000166579	Chromatin interaction
ENSG00000232310	Chromatin interaction
ENSG00000272273	Chromatin interaction
ENSG00000062822	Chromatin interaction
ENSG00000255717	Chromatin interaction
ENSG00000201699	Chromatin interaction
ENSG00000078237	Chromatin interaction
ENSG00000173451	Chromatin interaction
ENSG00000227723	Chromatin interaction
ENSG00000233396	Chromatin interaction

Extended variants
information (count: 7 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs1743961	0.82[ASN][1000 genomes]
rs1743963	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1763526	0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs1763528	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv492292	chr6:134464255-135028540	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
2	nsv1026369	chr6:134468470-135122264	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
3	nsv538444	chr6:134468470-135122264	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	81 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:134490600-134497400	Active TSS	Right Atrium	heart
2	chr6:134490600-134500200	Active TSS	Pancreatic Islets	Pancreatic Islet
3	chr6:134494000-134497200	Active TSS	Right Ventricle	heart
4	chr6:134494000-134497200	Active TSS	Stomach Mucosa	stomach
5	chr6:134494200-134497200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr6:134494200-134497200	Active TSS	Fetal Stomach	stomach
7	chr6:134494200-134497200	Active TSS	HSMMtube	muscle
8	chr6:134494400-134496400	Active TSS	Colonic Mucosa	Colon
9	chr6:134494400-134496800	Active TSS	Stomach Smooth Muscle	stomach
10	chr6:134494400-134497000	Active TSS	Fetal Intestine Small	intestine
11	chr6:134494400-134497200	Active TSS	Fetal Muscle Trunk	muscle
12	chr6:134494400-134497200	Active TSS	Lung	lung
13	chr6:134494400-134497200	Active TSS	NHLF	lung
14	chr6:134494400-134497400	Active TSS	Gastric	stomach
15	chr6:134494400-134497400	Active TSS	Pancreas	Pancrea
16	chr6:134494400-134497800	Active TSS	Esophagus	oesophagus
17	chr6:134494400-134498000	Active TSS	Ovary	ovary
18	chr6:134494400-134498600	Active TSS	Sigmoid Colon	Sigmoid Colon
19	chr6:134494400-134499600	Active TSS	Small Intestine	intestine
20	chr6:134494400-134500200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr6:134494600-134496800	Active TSS	Fetal Muscle Leg	muscle
22	chr6:134494600-134497000	Active TSS	iPS-15b Cell Line	embryonic stem cell
23	chr6:134494600-134497200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr6:134494600-134497200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
25	chr6:134494600-134498000	Active TSS	ES-I3 Cell Line	embryonic stem cell
26	chr6:134494600-134498200	Active TSS	Psoas Muscle	Psoas
27	chr6:134494600-134498400	Active TSS	Brain Angular Gyrus	brain
28	chr6:134494600-134499000	Active TSS	Duodenum Smooth Muscle	Duodenum
29	chr6:134494800-134496600	Active TSS	Fetal Thymus	thymus
30	chr6:134494800-134496600	Active TSS	Thymus	Thymus
31	chr6:134494800-134497000	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
32	chr6:134494800-134497000	Active TSS	Fetal Intestine Large	intestine
33	chr6:134494800-134497000	Active TSS	Placenta	Placenta
34	chr6:134494800-134497400	Active TSS	Left Ventricle	heart
35	chr6:134494800-134497400	Active TSS	A549	lung
36	chr6:134494800-134497800	Flanking Active TSS	Primary hematopoietic stem cells	blood
37	chr6:134494800-134497800	Active TSS	Brain Inferior Temporal Lobe	brain
38	chr6:134494800-134497800	Active TSS	Brain Substantia Nigra	brain
39	chr6:134495000-134496600	Active TSS	HMEC	breast
40	chr6:134495000-134496800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr6:134495000-134497000	Active TSS	iPS-18 Cell Line	embryonic stem cell
42	chr6:134495000-134497200	Active TSS	H1 Cell Line	embryonic stem cell
43	chr6:134495000-134497200	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr6:134495000-134497600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
45	chr6:134495000-134497600	Active TSS	NHDF-Ad	bronchial
46	chr6:134495000-134497800	Active TSS	H9 Cell Line	embryonic stem cell
47	chr6:134495000-134497800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr6:134495000-134497800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr6:134495000-134497800	Active TSS	Brain Cingulate Gyrus	brain
50	chr6:134495200-134496600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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