Variant report

Variant	rs2070215
Chromosome Location	chr7:99696797-99696798
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:36)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:36 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr7:99694417-99699772	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr7:99694703-99697612	GM12892	blood:	n/a	n/a
3	POLR2A	chr7:99696740-99696928	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr7:99694640-99696904	K562	blood:	n/a	n/a
5	POLR2A	chr7:99694653-99697678	H1-hESC	embryonic stem cell:	n/a	n/a
6	MXI1	chr7:99696123-99700530	SK-N-SH	brain:	n/a	chr7:99696168-99696177 chr7:99699039-99699048
7	POLR2A	chr7:99696453-99697702	HL-60	blood:	n/a	n/a
8	POLR2A	chr7:99696507-99696884	A549	lung:	n/a	n/a
9	HEY1	chr7:99694628-99697652	K562	blood:	n/a	chr7:99695196-99695205
10	POLR2A	chr7:99696030-99697157	SK-N-SH	brain:	n/a	n/a
11	POLR2A	chr7:99687998-99697728	H1-hESC	embryonic stem cell:	n/a	n/a
12	POLR2A	chr7:99696537-99696961	GM12891	blood:	n/a	n/a
13	POLR2A	chr7:99694683-99696815	K562	blood:	n/a	n/a
14	POLR2A	chr7:99696518-99697641	K562	blood:	n/a	n/a
15	POLR2A	chr7:99687562-99696983	HepG2	liver:	n/a	n/a
16	POLR2A	chr7:99694702-99697727	K562	blood:	n/a	n/a
17	POLR2A	chr7:99694608-99696959	Hela-S3	cervix:	n/a	n/a
18	CTCF	chr7:99696580-99696859	T-47D	breast:	n/a	n/a
19	POLR2A	chr7:99694646-99700079	PANC-1	pancreas:	n/a	n/a
20	POLR2A	chr7:99694505-99700789	H1-hESC	embryonic stem cell:	n/a	n/a
21	POLR2A	chr7:99696589-99696935	MCF-7	breast:	n/a	n/a
22	POLR2A	chr7:99696645-99696908	SK-N-SH	brain:	n/a	n/a
23	POLR2A	chr7:99694559-99697007	GM12892	blood:	n/a	n/a
24	POLR2A	chr7:99694635-99697617	K562	blood:	n/a	n/a
25	POLR2A	chr7:99694689-99697009	GM12892	blood:	n/a	n/a
26	POLR2A	chr7:99696641-99696952	Hela-S3	cervix:	n/a	n/a
27	POLR2A	chr7:99696511-99696944	GM12891	blood:	n/a	n/a
28	POLR2A	chr7:99696657-99696842	HepG2	liver:	n/a	n/a
29	POLR2A	chr7:99694793-99696820	K562	blood:	n/a	n/a
30	POLR2A	chr7:99694594-99699682	GM12878	blood:	n/a	n/a
31	POLR2A	chr7:99696495-99697017	H1-hESC	embryonic stem cell:	n/a	n/a
32	POLR2A	chr7:99696694-99697351	HUVEC	blood vessel:	n/a	n/a
33	ATF2	chr7:99696441-99697189	H1-hESC	embryonic stem cell:	n/a	n/a
34	POLR2A	chr7:99696598-99697015	ECC-1	luminal epithelium:	n/a	n/a
35	POLR2A	chr7:99694577-99700301	SK-N-MC	brain:	n/a	n/a
36	POLR2A	chr7:99696355-99697688	GM12878	blood:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:99696160..99700887-chr7:99753963..99757907,5	K562	blood:
2	chr7:99695452..99699124-chr7:100025277..100027831,3	MCF-7	breast:
3	chr7:99696160..99699295-chr7:99753963..99757907,4	K562	blood:
4	chr7:99645952..99651427-chr7:99695296..99699701,5	K562	blood:
5	chr7:99696789..99700792-chr7:100024893..100031468,10	K562	blood:
6	chr7:99645798..99648883-chr7:99696634..99699359,3	MCF-7	breast:
7	chr7:99061682..99064704-chr7:99696557..99699487,3	K562	blood:
8	chr7:99696142..99700081-chr7:99754300..99760427,7	MCF-7	breast:
9	chr17:56734803..56736757-chr7:99696174..99697894,2	MCF-7	breast:

No data

Variant related genes	Relation type
MCM7	TF binding region
AP4M1	TF binding region
ENSG00000166529	Chromatin interaction
ENSG00000146826	Chromatin interaction
ENSG00000202077	Chromatin interaction
ENSG00000078487	Chromatin interaction
ENSG00000241468	Chromatin interaction
ENSG00000266154	Chromatin interaction
ENSG00000106246	Chromatin interaction
ENSG00000146834	Chromatin interaction
ENSG00000248919	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10228764	0.90[EUR][1000 genomes]
rs10267212	0.82[CEU][hapmap]
rs10281368	1.00[CEU][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs1060544	0.90[EUR][1000 genomes]
rs1076237	0.81[CEU][hapmap]
rs11771139	0.94[TSI][hapmap]
rs12705070	1.00[CEU][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs12705071	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13223792	1.00[CEU][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs13232115	0.88[EUR][1000 genomes]
rs1534310	0.99[EUR][1000 genomes]
rs1880949	0.97[TSI][hapmap]
rs2293479	0.91[CEU][hapmap];0.85[EUR][1000 genomes]
rs34031156	0.95[EUR][1000 genomes]
rs35146811	0.97[TSI][hapmap]
rs4134903	0.95[CEU][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs4424195	1.00[CEU][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs4729576	0.96[EUR][1000 genomes]
rs59261051	0.95[EUR][1000 genomes]
rs6465760	0.82[CEU][hapmap]
rs6465761	0.90[EUR][1000 genomes]
rs6465762	0.90[EUR][1000 genomes]
rs6950205	0.94[EUR][1000 genomes]
rs6953441	0.90[EUR][1000 genomes]
rs6974305	0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1829865	chr7:99430678-99755141	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1131 gene(s)	inside rSNPs	diseases
2	esv1830649	chr7:99430678-99755141	Strong transcription Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1131 gene(s)	inside rSNPs	diseases
3	nsv534298	chr7:99478011-99886076	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1132 gene(s)	inside rSNPs	diseases
4	nsv469687	chr7:99572543-99755141	Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1115 gene(s)	inside rSNPs	diseases
5	nsv482601	chr7:99572543-99755141	Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1115 gene(s)	inside rSNPs	diseases
6	nsv607931	chr7:99664817-99796146	Bivalent Enhancer Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Active TSS Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1097 gene(s)	inside rSNPs	diseases
7	esv1798486	chr7:99689883-99930879	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1085 gene(s)	inside rSNPs	diseases
8	esv1833059	chr7:99689883-99930879	Flanking Active TSS Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1085 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs2070215	GATS	cis	lymphoblastoid	seeQTL
rs2070215	GAL3ST4	cis	cerebellum	SCAN
rs2070215	SERPINE1	cis	cerebellum	SCAN
rs2070215	GATS	cis	cerebellum	SCAN
rs2070215	ZSCAN21	cis	parietal	SCAN
rs2070215	GATS	cis	parietal	SCAN
rs2070215	ZNF498	cis	cerebellum	SCAN
rs2070215	BUD31	cis	parietal	SCAN
rs2070215	PILRB	cis	parietal	SCAN
rs2070215	ZKSCAN1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:99687400-99697200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr7:99687600-99696800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
3	chr7:99688000-99696800	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr7:99688000-99696800	Strong transcription	Primary monocytes fromperipheralblood	blood
5	chr7:99688000-99696800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
6	chr7:99688000-99696800	Strong transcription	Brain Angular Gyrus	brain
7	chr7:99688000-99697000	Strong transcription	HUES6 Cell Line	embryonic stem cell
8	chr7:99688000-99697000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr7:99688000-99697000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr7:99688000-99697000	Strong transcription	A549	lung
11	chr7:99688000-99697000	Strong transcription	Monocytes-CD14+_RO01746	blood
12	chr7:99688000-99697200	Strong transcription	iPS-15b Cell Line	embryonic stem cell
13	chr7:99688000-99697200	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr7:99688000-99697200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
15	chr7:99688000-99697200	Strong transcription	Brain Anterior Caudate	brain
16	chr7:99688000-99697200	Strong transcription	Brain Hippocampus Middle	brain
17	chr7:99688000-99697200	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr7:99688000-99697200	Strong transcription	Left Ventricle	heart
19	chr7:99688000-99697200	Strong transcription	Ovary	ovary
20	chr7:99688000-99697200	Strong transcription	NHEK	skin
21	chr7:99688200-99696800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr7:99688200-99696800	Strong transcription	Placenta Amnion	Placenta Amnion
23	chr7:99688200-99697000	Strong transcription	Brain Cingulate Gyrus	brain
24	chr7:99688200-99697200	Strong transcription	ES-I3 Cell Line	embryonic stem cell
25	chr7:99688200-99697200	Strong transcription	Brain Substantia Nigra	brain
26	chr7:99688200-99697400	Strong transcription	Sigmoid Colon	Sigmoid Colon
27	chr7:99688400-99696800	Strong transcription	Colonic Mucosa	Colon
28	chr7:99688400-99696800	Strong transcription	Colon Smooth Muscle	Colon
29	chr7:99688600-99697400	Strong transcription	Aorta	Aorta
30	chr7:99689000-99697200	Strong transcription	HMEC	breast
31	chr7:99689000-99697200	Strong transcription	Osteobl	bone
32	chr7:99689200-99697000	Strong transcription	NHDF-Ad	bronchial
33	chr7:99689200-99697200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr7:99689400-99697000	Strong transcription	Muscle Satellite Cultured Cells	--
35	chr7:99689400-99697200	Weak transcription	Right Atrium	heart
36	chr7:99691600-99697000	Strong transcription	Brain Inferior Temporal Lobe	brain
37	chr7:99691600-99697000	Strong transcription	Rectal Smooth Muscle	rectum
38	chr7:99691800-99696800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr7:99691800-99696800	Strong transcription	Lung	lung
40	chr7:99691800-99697200	Strong transcription	NHLF	lung
41	chr7:99692000-99696800	Strong transcription	Esophagus	oesophagus
42	chr7:99692000-99696800	Strong transcription	Placenta	Placenta
43	chr7:99692000-99697000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr7:99692000-99697000	Strong transcription	Right Ventricle	heart
45	chr7:99692000-99697000	Strong transcription	Skeletal Muscle Male	skeletal muscle
46	chr7:99692200-99697000	Strong transcription	Adipose Nuclei	Adipose
47	chr7:99692800-99696800	Strong transcription	HSMMtube	muscle
48	chr7:99693400-99696800	Strong transcription	Psoas Muscle	Psoas
49	chr7:99693400-99697600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
50	chr7:99694800-99696800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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