Variant report

Variant	rs7537508
Chromosome Location	chr1:174970505-174970506
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:174188636..174191430-chr1:174968395..174970624,2	K562	blood:
2	chr1:174968752..174972930-chr1:174980465..174984788,7	MCF-7	breast:
3	chr1:173835653..173838766-chr1:174968504..174972418,4	K562	blood:
4	chr1:174967181..174971270-chr1:174989768..174994107,8	MCF-7	breast:
5	chr1:174944704..174946274-chr1:174968716..174970697,2	MCF-7	breast:
6	chr1:174966903..174971287-chr1:174971534..174977740,10	MCF-7	breast:
7	chr1:174966455..174979047-chr1:174985921..174994239,29	MCF-7	breast:
8	chr1:174968288..174970676-chr11:69455008..69457923,2	MCF-7	breast:
9	chr1:174818265..174820720-chr1:174969337..174970845,2	K562	blood:
10	chr1:174968308..174972682-chr1:174973669..174977278,7	MCF-7	breast:
11	chr1:174967096..174970659-chr1:174981028..174985682,6	MCF-7	breast:
12	chr1:174968082..174970631-chr17:57918562..57920728,2	MCF-7	breast:
13	chr1:174933583..174936463-chr1:174967523..174970706,3	MCF-7	breast:
14	chr1:174927580..174945830-chr1:174955726..174971213,32	K562	blood:

No data

Variant related genes	Relation type
ENSG00000231378	Chromatin interaction
ENSG00000152061	Chromatin interaction
ENSG00000110092	Chromatin interaction
ENSG00000234741	Chromatin interaction
ENSG00000116161	Chromatin interaction
ENSG00000199004	Chromatin interaction
ENSG00000120333	Chromatin interaction
ENSG00000185278	Chromatin interaction
ENSG00000206659	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10912860	0.95[CEU][hapmap];1.00[CHB][hapmap];0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10912867	0.90[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11582831	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12119351	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12122361	1.00[CHB][hapmap];0.96[TSI][hapmap]
rs12122399	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12124150	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12125682	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12723394	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12753457	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34484492	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56978149	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59663317	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6691857	1.00[CHB][hapmap]
rs6700816	1.00[CHB][hapmap]
rs7550448	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001000	chr1:174944208-174978853	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7537508	GPR52	cis	parietal	SCAN
rs7537508	RC3H1	Cis_chr	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:174967400-174970600	Active TSS	iPS-18 Cell Line	embryonic stem cell
2	chr1:174967400-174971400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr1:174967400-174971400	Active TSS	GM12878-XiMat	blood
4	chr1:174967600-174970600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr1:174967600-174970600	Active TSS	HUES64 Cell Line	embryonic stem cell
6	chr1:174967600-174970600	Active TSS	iPS-15b Cell Line	embryonic stem cell
7	chr1:174967600-174970600	Active TSS	Brain Inferior Temporal Lobe	brain
8	chr1:174967600-174970600	Active TSS	Fetal Brain Female	brain
9	chr1:174967600-174970800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr1:174967600-174971200	Active TSS	A549	lung
11	chr1:174967600-174971600	Active TSS	HUES48 Cell Line	embryonic stem cell
12	chr1:174967600-174971600	Active TSS	HUES6 Cell Line	embryonic stem cell
13	chr1:174967800-174970600	Active TSS	H1 Cell Line	embryonic stem cell
14	chr1:174967800-174970600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr1:174967800-174970600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr1:174967800-174970800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr1:174967800-174970800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr1:174967800-174970800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr1:174967800-174971000	Active TSS	H9 Cell Line	embryonic stem cell
20	chr1:174967800-174971400	Active TSS	iPS-20b Cell Line	embryonic stem cell
21	chr1:174968000-174970600	Active TSS	Ovary	ovary
22	chr1:174968200-174970600	Active TSS	Fetal Thymus	thymus
23	chr1:174968200-174971800	Active TSS	K562	blood
24	chr1:174968400-174970600	Active TSS	Primary T helper naive cells from peripheral blood	blood
25	chr1:174968400-174970600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr1:174968400-174970600	Active TSS	Fetal Intestine Small	intestine
27	chr1:174968400-174970600	Active TSS	Stomach Smooth Muscle	stomach
28	chr1:174968400-174970600	Active TSS	Hela-S3	cervix
29	chr1:174968400-174970600	Active TSS	HMEC	breast
30	chr1:174968400-174970600	Active TSS	NHDF-Ad	bronchial
31	chr1:174969200-174970600	Flanking Active TSS	Primary B cells from cord blood	blood
32	chr1:174969400-174970600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr1:174969400-174970800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
34	chr1:174969400-174971000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr1:174969600-174970600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
36	chr1:174969600-174970600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr1:174969600-174970800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr1:174969600-174971200	Active TSS	Brain Germinal Matrix	brain
39	chr1:174969800-174970600	Flanking Active TSS	Fetal Kidney	kidney
40	chr1:174969800-174970600	Weak transcription	Spleen	Spleen
41	chr1:174969800-174970800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr1:174969800-174970800	Flanking Active TSS	Primary T cells from cord blood	blood
43	chr1:174969800-174970800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
44	chr1:174969800-174970800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr1:174969800-174970800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr1:174969800-174970800	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
47	chr1:174969800-174970800	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
48	chr1:174969800-174970800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
49	chr1:174969800-174972200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr1:174969800-174981600	Weak transcription	Gastric	stomach

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