Variant report

Variant	rs5002508
Chromosome Location	chr12:74933868-74933869
allele	A/C
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	chr12:74931200-74936073	HepG2	liver:	n/a	n/a
2	POLR2A	chr12:74933848-74934267	HepG2	liver:	n/a	n/a
3	HA-E2F1	chr12:74931278-74933877	MCF-7	breast:	n/a	chr12:74931774-74931784 chr12:74931773-74931782 chr12:74931642-74931649 chr12:74931547-74931556
4	MXI1	chr12:74930680-74934315	SK-N-SH	brain:	n/a	chr12:74932789-74932798
5	POLR2A	chr12:74933579-74933911	K562	blood:	n/a	n/a
6	MAFF	chr12:74933753-74934165	K562	blood:	n/a	n/a
7	CUX1	chr12:74933797-74934313	K562	blood:	n/a	n/a
8	POLR2A	chr12:74931110-74940575	MCF10A-Er-Src	breast:	n/a	n/a
9	POLR2A	chr12:74931116-74935658	SK-N-MC	brain:	n/a	n/a
10	POLR2A	chr12:74931201-74935166	GM12878	blood:	n/a	n/a
11	MXI1	chr12:74933849-74933930	GM12878	blood:	n/a	n/a
12	WRNIP1	chr12:74931153-74935222	GM12878	blood:	n/a	n/a
13	MAFK	chr12:74933809-74934176	K562	blood:	n/a	n/a
14	POLR2A	chr12:74931269-74934114	Hela-S3	cervix:	n/a	n/a
15	POLR2A	chr12:74932372-74934585	K562	blood:	n/a	n/a
16	POLR2A	chr12:74933517-74933889	Hela-S3	cervix:	n/a	n/a
17	JUND	chr12:74933868-74934153	K562	blood:	n/a	n/a
18	POLR2A	chr12:74931126-74935588	GM12878	blood:	n/a	n/a
19	POLR2A	chr12:74932912-74937655	MCF10A-Er-Src	breast:	n/a	n/a
20	POLR2A	chr12:74931035-74936789	IMR90	lung:	n/a	n/a
21	POLR2A	chr12:74932414-74936105	A549	lung:	n/a	n/a
22	POLR2A	chr12:74931091-74937173	GM12891	blood:	n/a	n/a
23	POLR2A	chr12:74931368-74933966	HUVEC	blood vessel:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:74686465..74688529-chr12:74932040..74934610,2	K562	blood:
2	chr12:74933499..74938752-chr12:74938991..74943644,10	K562	blood:

Variant related genes	Relation type
ENSG00000257386	TF binding region
ENSG00000251138	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10506696	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12298502	0.89[EUR][1000 genomes]
rs1389488	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17113550	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17113561	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17113703	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17113716	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17113730	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17113736	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17113745	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17113753	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17179283	0.98[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs17179465	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17772239	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2605378	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2613897	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2613898	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4550284	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1039468	chr12:74080586-75000246	Weak transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv899292	chr12:74835107-74934162	Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Genic enhancers Enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
3	nsv899293	chr12:74835107-74995760	Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
4	nsv899295	chr12:74854750-74984992	Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
5	nsv470303	chr12:74880668-74945356	Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	n/a
6	nsv899296	chr12:74880668-74974630	Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	5 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	chr12:74931200-74934000	Active TSS	H9 Cell Line	embryonic stem cell
2	chr12:74931800-74934000	Transcr. at gene 5' and 3'	Muscle Satellite Cultured Cells	--
3	chr12:74932000-74934000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
4	chr12:74932000-74934400	Flanking Active TSS	Adipose Nuclei	Adipose
5	chr12:74932000-74934400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
6	chr12:74932000-74935000	Transcr. at gene 5' and 3'	Fetal Lung	lung
7	chr12:74932200-74934000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
8	chr12:74932200-74934000	Flanking Active TSS	NH-A	brain
9	chr12:74932200-74934800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
10	chr12:74932200-74935200	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
11	chr12:74932400-74934000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
12	chr12:74932400-74934000	Flanking Active TSS	Brain Substantia Nigra	brain
13	chr12:74932400-74934200	Transcr. at gene 5' and 3'	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr12:74932400-74934200	Flanking Active TSS	Liver	Liver
15	chr12:74932400-74934200	Flanking Active TSS	Fetal Brain Male	brain
16	chr12:74932400-74934200	Flanking Active TSS	HUVEC	blood vessel
17	chr12:74932400-74934200	Transcr. at gene 5' and 3'	NHLF	lung
18	chr12:74932400-74934400	Transcr. at gene 5' and 3'	Fetal Stomach	stomach
19	chr12:74932400-74934600	Flanking Active TSS	Brain Angular Gyrus	brain
20	chr12:74932400-74934800	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
21	chr12:74932400-74934800	Flanking Active TSS	Brain Cingulate Gyrus	brain
22	chr12:74932400-74934800	Flanking Active TSS	Thymus	Thymus
23	chr12:74932400-74935000	Transcr. at gene 5' and 3'	A549	lung
24	chr12:74932400-74935200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr12:74932400-74935200	Transcr. at gene 5' and 3'	Dnd41	blood
26	chr12:74932400-74935400	Transcr. at gene 5' and 3'	NHEK	skin
27	chr12:74932600-74934400	Transcr. at gene 5' and 3'	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr12:74932600-74934400	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
29	chr12:74932600-74934600	Transcr. at gene 5' and 3'	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr12:74932600-74934600	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
31	chr12:74932600-74934600	Transcr. at gene 5' and 3'	Fetal Muscle Leg	muscle
32	chr12:74932600-74934800	Flanking Active TSS	Fetal Heart	heart
33	chr12:74932600-74934800	Enhancers	Spleen	Spleen
34	chr12:74932600-74935000	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells short term culture	blood
35	chr12:74932600-74935000	Transcr. at gene 5' and 3'	K562	blood
36	chr12:74932600-74935200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr12:74932600-74935200	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr12:74932600-74935600	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
39	chr12:74932600-74935800	Transcr. at gene 5' and 3'	Fetal Brain Female	brain
40	chr12:74932800-74934000	Transcr. at gene 5' and 3'	Fetal Intestine Small	intestine
41	chr12:74932800-74934200	Transcr. at gene 5' and 3'	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr12:74932800-74934200	Enhancers	Ovary	ovary
43	chr12:74932800-74934200	Transcr. at gene 5' and 3'	HSMM	muscle
44	chr12:74932800-74934200	Transcr. at gene 5' and 3'	NHDF-Ad	bronchial
45	chr12:74932800-74934400	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr12:74932800-74934400	Transcr. at gene 5' and 3'	Fetal Adrenal Gland	Adrenal Gland
47	chr12:74932800-74934400	Enhancers	Small Intestine	intestine
48	chr12:74932800-74934600	Transcr. at gene 5' and 3'	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr12:74932800-74934600	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr12:74932800-74934600	Transcr. at gene 5' and 3'	Foreskin Melanocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links