Variant report

Variant	rs34257469
Chromosome Location	chr7:99150185-99150186
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	POLR2A	chr7:99149121-99150224	SK-N-MC	brain:	n/a	n/a
2	POLR2A	chr7:99149373-99150205	U87	brain:	n/a	n/a
3	REST	chr7:99148964-99150308	H1-neurons	neurons:	n/a	chr7:99149870-99149890 chr7:99149505-99149512 chr7:99149503-99149512
4	IRF3	chr7:99150173-99150363	GM12878	blood:	n/a	n/a
5	EP300	chr7:99149595-99150272	K562	blood:	n/a	chr7:99149743-99149750 chr7:99149873-99149889
6	POLR2A	chr7:99149329-99150438	GM12891	blood:	n/a	n/a
7	GATA3	chr7:99149249-99150208	A549	lung:	n/a	n/a
8	HCFC1	chr7:99149379-99150223	Hela-S3	cervix:	n/a	n/a
9	STAT5A	chr7:99149419-99150278	K562	blood:	n/a	n/a
10	MXI1	chr7:99149353-99150209	GM12878	blood:	n/a	n/a
11	POLR2A	chr7:99149367-99150249	U87	brain:	n/a	n/a
12	GABPA	chr7:99148816-99150611	MCF-7	breast:	n/a	n/a
13	ELF1	chr7:99149393-99150211	HCT-116	colon:	n/a	chr7:99149741-99149750 chr7:99149740-99149751
14	POLR2A	chr7:99149355-99150244	H1-neurons	neurons:	n/a	n/a
15	CREB1	chr7:99149130-99150242	K562	blood:	n/a	n/a
16	POLR2A	chr7:99149156-99150195	PFSK-1	brain:	n/a	n/a
17	NFATC1	chr7:99149389-99150257	GM12878	blood:	n/a	n/a
18	GABPA	chr7:99149140-99150325	A549	lung:	n/a	n/a
19	NRF1	chr7:99149004-99150531	SK-N-SH	brain:	n/a	n/a
20	POLR2A	chr7:99148800-99150574	HepG2	liver:	n/a	n/a
21	ZNF263	chr7:99149331-99150245	HEK293-T-REx	kidney:	n/a	n/a
22	SP2	chr7:99149379-99150188	HepG2	liver:	n/a	n/a
23	PML	chr7:99149303-99150228	GM12878	blood:	n/a	n/a
24	GABPA	chr7:99149099-99150378	A549	lung:	n/a	n/a
25	POLR2A	chr7:99149031-99150348	SK-N-SH	brain:	n/a	n/a
26	GABPA	chr7:99149221-99150459	SK-N-SH	brain:	n/a	n/a
27	GABPA	chr7:99149125-99150268	HL-60	blood:	n/a	n/a
28	GABPA	chr7:99149196-99150616	SK-N-SH	brain:	n/a	n/a
29	SIN3AK20	chr7:99149098-99150228	MCF-7	breast:	n/a	n/a
30	HEY1	chr7:99149125-99150236	K562	blood:	n/a	n/a
31	CREB1	chr7:99149274-99150275	GM12878	blood:	n/a	n/a
32	NRF1	chr7:99149600-99150263	GM12878	blood:	n/a	n/a
33	GABPA	chr7:99149229-99150193	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr7:99148561..99151367-chr7:99213024..99215918,3	K562	blood:
2	chr7:99148330..99152549-chr7:99153303..99160203,7	MCF-7	breast:
3	chr7:99149750..99151716-chr7:99212899..99215707,2	K562	blood:
4	chr7:99147270..99151762-chr7:99212930..99216791,5	MCF-7	breast:
5	chr7:99149727..99150416-chr8:134308958..134309544,2	Hela-S3	cervix:
6	chr7:99147703..99150655-chr7:99214369..99216200,3	MCF-7	breast:
7	chr7:99097512..99099294-chr7:99149629..99151272,2	K562	blood:

Variant related genes	Relation type
FAM200A	TF binding region
ENSG00000197343	Chromatin interaction
ENSG00000104419	Chromatin interaction
ENSG00000272647	Chromatin interaction
ENSG00000221909	Chromatin interaction
ENSG00000197037	Chromatin interaction
ENSG00000160908	Chromatin interaction

Extended variants
information (count: 78 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs10215765	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10215854	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.98[LWK][hapmap];0.89[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10226310	0.89[CEU][hapmap];1.00[CHB][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10229886	1.00[ASN][1000 genomes]
rs10230784	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10235235	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.84[TSI][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10236240	1.00[ASN][1000 genomes]
rs10264505	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10268984	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs10273424	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10275381	1.00[ASN][1000 genomes]
rs10277447	1.00[ASN][1000 genomes]
rs10278040	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs10808111	0.89[CEU][hapmap];1.00[CHB][hapmap];0.86[EUR][1000 genomes]
rs10808112	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10953288	0.89[CEU][hapmap];1.00[CHB][hapmap];0.84[TSI][hapmap];1.00[ASN][1000 genomes]
rs10953289	1.00[ASN][1000 genomes]
rs11555142	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11761528	1.00[CHB][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11766423	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11971640	1.00[ASN][1000 genomes]
rs11973173	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11973801	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11974593	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs11978345	1.00[ASN][1000 genomes]
rs11978582	1.00[ASN][1000 genomes]
rs11980995	1.00[ASN][1000 genomes]
rs11980999	1.00[ASN][1000 genomes]
rs11983474	1.00[ASN][1000 genomes]
rs12531852	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[TSI][hapmap];1.00[ASN][1000 genomes]
rs12533251	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12535424	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12536002	1.00[ASN][1000 genomes]
rs12538826	0.81[EUR][1000 genomes]
rs12539480	1.00[ASN][1000 genomes]
rs13223272	1.00[ASN][1000 genomes]
rs13227522	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13240600	0.81[CEU][hapmap]
rs13243267	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.84[TSI][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17161687	1.00[ASN][1000 genomes]
rs17161761	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.84[TSI][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2003498	1.00[ASN][1000 genomes]
rs28371764	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs28419687	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28602855	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28627543	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28862110	0.86[CEU][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap]
rs28988579	1.00[ASN][1000 genomes]
rs34096782	1.00[ASN][1000 genomes]
rs34111611	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs34967184	1.00[ASN][1000 genomes]
rs35183025	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35296070	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs35656351	1.00[ASN][1000 genomes]
rs36104094	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3779354	0.90[YRI][hapmap]
rs45618033	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4765	1.00[ASN][1000 genomes]
rs57980352	1.00[ASN][1000 genomes]
rs58964157	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60577432	1.00[ASN][1000 genomes]
rs66478766	1.00[ASN][1000 genomes]
rs66509940	0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66568021	1.00[ASN][1000 genomes]
rs67546174	1.00[ASN][1000 genomes]
rs67909852	1.00[ASN][1000 genomes]
rs6947826	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.84[TSI][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6947941	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.84[TSI][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6947974	0.89[CEU][hapmap];1.00[CHB][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6955891	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6960810	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[TSI][hapmap];1.00[ASN][1000 genomes]
rs704798	1.00[ASN][1000 genomes]
rs73163167	1.00[ASN][1000 genomes]
rs73163169	1.00[ASN][1000 genomes]
rs740160	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs7778859	1.00[ASN][1000 genomes]
rs9632722	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9656060	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs34257469	GS1-259H13.2	cis	Thyroid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:99148200-99150400	Active TSS	HUES6 Cell Line	embryonic stem cell
2	chr7:99148400-99150200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr7:99148400-99150200	Active TSS	HSMM	muscle
4	chr7:99148600-99150200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr7:99148600-99150200	Active TSS	Right Ventricle	heart
6	chr7:99148600-99150400	Active TSS	ES-I3 Cell Line	embryonic stem cell
7	chr7:99148600-99150400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr7:99148600-99150400	Active TSS	HUES48 Cell Line	embryonic stem cell
9	chr7:99148600-99150400	Active TSS	HUES64 Cell Line	embryonic stem cell
10	chr7:99148600-99150400	Active TSS	Fetal Intestine Large	intestine
11	chr7:99148600-99150600	Active TSS	iPS-18 Cell Line	embryonic stem cell
12	chr7:99148800-99150200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr7:99148800-99150200	Active TSS	H9 Cell Line	embryonic stem cell
14	chr7:99148800-99150200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr7:99148800-99150200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr7:99148800-99150200	Active TSS	Breast Myoepithelial Primary Cells	Breast
17	chr7:99148800-99150200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr7:99148800-99150200	Active TSS	Left Ventricle	heart
19	chr7:99148800-99150200	Active TSS	Ovary	ovary
20	chr7:99148800-99150200	Active TSS	Hela-S3	cervix
21	chr7:99148800-99150200	Active TSS	NHLF	lung
22	chr7:99148800-99150400	Active TSS	iPS-15b Cell Line	embryonic stem cell
23	chr7:99148800-99150400	Active TSS	iPS-20b Cell Line	embryonic stem cell
24	chr7:99148800-99150400	Active TSS	Pancreatic Islets	Pancreatic Islet
25	chr7:99148800-99150400	Active TSS	Psoas Muscle	Psoas
26	chr7:99148800-99150400	Active TSS	Right Atrium	heart
27	chr7:99148800-99150600	Active TSS	A549	lung
28	chr7:99149000-99150200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr7:99149000-99150200	Active TSS	Aorta	Aorta
30	chr7:99149000-99150200	Active TSS	Colon Smooth Muscle	Colon
31	chr7:99149000-99150200	Active TSS	Duodenum Smooth Muscle	Duodenum
32	chr7:99149000-99150200	Active TSS	Fetal Heart	heart
33	chr7:99149000-99150200	Active TSS	Fetal Stomach	stomach
34	chr7:99149000-99150400	Active TSS	Fetal Intestine Small	intestine
35	chr7:99149000-99150400	Active TSS	Rectal Smooth Muscle	rectum
36	chr7:99149000-99150600	Active TSS	Muscle Satellite Cultured Cells	--
37	chr7:99149000-99150600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr7:99149200-99150200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
39	chr7:99149200-99150200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr7:99149200-99150200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr7:99149200-99150200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
42	chr7:99149200-99150200	Active TSS	Fetal Adrenal Gland	Adrenal Gland
43	chr7:99149200-99150200	Active TSS	Fetal Brain Female	brain
44	chr7:99149200-99150200	Active TSS	Placenta	Placenta
45	chr7:99149200-99150200	Active TSS	Stomach Mucosa	stomach
46	chr7:99149200-99150400	Active TSS	Duodenum Mucosa	Duodenum
47	chr7:99149400-99150200	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
48	chr7:99149400-99150200	Active TSS	Fetal Muscle Trunk	muscle
49	chr7:99149400-99150400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr7:99149600-99150200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood

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