Variant report

Variant	rs7624987
Chromosome Location	chr3:99352912-99352913
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	JUND	chr3:99352729-99353213	H1-hESC	embryonic stem cell:	n/a	chr3:99353124-99353135 chr3:99352935-99352945 chr3:99353126-99353135 chr3:99353125-99353134 chr3:99353126-99353134 chr3:99353127-99353134 chr3:99352935-99352945
2	MYC	chr3:99352772-99353025	MCF10A-Er-Src	breast:	n/a	n/a
3	JUN	chr3:99352782-99353202	HUVEC	blood vessel:	n/a	chr3:99352935-99352945 chr3:99353126-99353135 chr3:99353125-99353134 chr3:99353126-99353134 chr3:99353127-99353134 chr3:99352935-99352945
4	STAT3	chr3:99352792-99353116	MCF10A-Er-Src	breast:	n/a	n/a
5	FOS	chr3:99352747-99353330	MCF10A-Er-Src	breast:	n/a	chr3:99352935-99352945 chr3:99353126-99353135 chr3:99353125-99353134 chr3:99353126-99353134 chr3:99353127-99353134 chr3:99352935-99352945
6	FOS	chr3:99352771-99353304	MCF10A-Er-Src	breast:	n/a	chr3:99352935-99352945 chr3:99353126-99353135 chr3:99353125-99353134 chr3:99353126-99353134 chr3:99353127-99353134 chr3:99352935-99352945
7	MYC	chr3:99352795-99353121	MCF10A-Er-Src	breast:	n/a	n/a
8	POLR2A	chr3:99352814-99352997	MCF10A-Er-Src	breast:	n/a	n/a
9	FOS	chr3:99352756-99353285	MCF10A-Er-Src	breast:	n/a	chr3:99352935-99352945 chr3:99353126-99353135 chr3:99353125-99353134 chr3:99353126-99353134 chr3:99353127-99353134 chr3:99352935-99352945
10	POLR2A	chr3:99352608-99353206	HUVEC	blood vessel:	n/a	n/a
11	FOS	chr3:99352764-99353220	HUVEC	blood vessel:	n/a	chr3:99352935-99352945 chr3:99353126-99353135 chr3:99353125-99353134 chr3:99353126-99353134 chr3:99353127-99353134 chr3:99352935-99352945
12	STAT3	chr3:99352685-99353048	MCF10A-Er-Src	breast:	n/a	n/a
13	EP300	chr3:99352774-99353474	ECC-1	luminal epithelium:	n/a	chr3:99353125-99353134 chr3:99353126-99353135
14	SRF	chr3:99352823-99353304	ECC-1	luminal epithelium:	n/a	chr3:99353080-99353095 chr3:99353079-99353096
15	STAT3	chr3:99352794-99353053	MCF10A-Er-Src	breast:	n/a	n/a
16	FOS	chr3:99352761-99353300	MCF10A-Er-Src	breast:	n/a	chr3:99352935-99352945 chr3:99353126-99353135 chr3:99353125-99353134 chr3:99353126-99353134 chr3:99353127-99353134 chr3:99352935-99352945

Variant related genes	Relation type
COL8A1	TF binding region

Extended variants
information (count: 15 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs12107500	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12486836	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12487332	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12495115	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12495263	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12496018	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1418975	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs16841583	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17777228	0.92[CEU][hapmap];0.86[YRI][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73150246	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73150248	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7645927	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7653590	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9849369	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9942067	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7624987	COL8A1	cis	cerebellum	SCAN
rs7624987	DCBLD2	cis	cerebellum	SCAN

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:99346400-99355800	Weak transcription	Hela-S3	cervix
2	chr3:99347200-99355800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr3:99349800-99354000	Enhancers	iPS-15b Cell Line	embryonic stem cell
4	chr3:99350200-99353800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr3:99350400-99354000	Weak transcription	HMEC	breast
6	chr3:99350600-99354400	Enhancers	H1 Cell Line	embryonic stem cell
7	chr3:99351400-99353600	Enhancers	iPS-18 Cell Line	embryonic stem cell
8	chr3:99351400-99355200	Enhancers	ES-I3 Cell Line	embryonic stem cell
9	chr3:99351600-99353600	Enhancers	HUES6 Cell Line	embryonic stem cell
10	chr3:99351800-99353400	Enhancers	Fetal Intestine Large	intestine
11	chr3:99351800-99354200	Enhancers	H9 Cell Line	embryonic stem cell
12	chr3:99352000-99354400	Enhancers	HUES64 Cell Line	embryonic stem cell
13	chr3:99352000-99354800	Enhancers	HUES48 Cell Line	embryonic stem cell
14	chr3:99352200-99353800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr3:99352200-99353800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr3:99352200-99354200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
17	chr3:99352400-99355400	Enhancers	HUVEC	blood vessel
18	chr3:99352600-99353600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr3:99352600-99354200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr3:99352600-99354800	Enhancers	NH-A	brain
21	chr3:99352800-99353000	Enhancers	iPS-20b Cell Line	embryonic stem cell
22	chr3:99352800-99353000	Enhancers	Fetal Kidney	kidney
23	chr3:99352800-99353000	Enhancers	NHLF	lung
24	chr3:99352800-99353400	Enhancers	Muscle Satellite Cultured Cells	--
25	chr3:99352800-99353400	Enhancers	NHEK	skin
26	chr3:99352800-99353600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
27	chr3:99352800-99353800	Enhancers	Aorta	Aorta
28	chr3:99352800-99354000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr3:99352800-99354600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr3:99352800-99355800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links