Variant report

Variant	rs62490312
Chromosome Location	chr7:150800485-150800486
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:150799677..150803101-chr7:150803816..150805477,3	MCF-7	breast:
2	chr7:150795047..150796813-chr7:150798613..150800865,2	MCF-7	breast:

Extended variants
information (count: 31 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10227172	0.82[ASN][1000 genomes]
rs12670760	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13225215	0.84[ASN][1000 genomes]
rs13239507	0.84[ASN][1000 genomes]
rs1978655	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28645628	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4725388	0.81[ASN][1000 genomes]
rs4725990	0.88[ASN][1000 genomes]
rs60987133	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs6464124	0.83[ASN][1000 genomes]
rs6464125	0.84[ASN][1000 genomes]
rs6464126	0.84[ASN][1000 genomes]
rs749318	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs749319	0.94[ASN][1000 genomes]
rs7783954	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1821419	chr7:150593315-150974269	Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	128 gene(s)	inside rSNPs	diseases
2	nsv889465	chr7:150640285-150800823	Flanking Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
3	nsv1028645	chr7:150643928-150806534	Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	59 gene(s)	inside rSNPs	diseases
4	nsv539198	chr7:150643928-150879259	Weak transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	72 gene(s)	inside rSNPs	diseases
5	nsv889476	chr7:150729212-150951819	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	120 gene(s)	inside rSNPs	diseases
6	nsv889477	chr7:150731698-150837529	Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	57 gene(s)	inside rSNPs	diseases
7	nsv889478	chr7:150732812-150889527	Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	61 gene(s)	inside rSNPs	diseases
8	nsv831188	chr7:150735204-150912875	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
9	nsv465214	chr7:150751590-150822192	Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Strong transcription Weak transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
10	nsv609012	chr7:150751590-150822192	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
11	nsv609013	chr7:150751590-150832913	Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
12	nsv465215	chr7:150762871-150825087	Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
13	nsv609014	chr7:150762871-150825087	Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
14	nsv889481	chr7:150766799-150837529	Weak transcription Genic enhancers Flanking Active TSS Active TSS Strong transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
15	nsv889482	chr7:150766799-150851566	Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
16	nsv889486	chr7:150775306-150891641	Enhancers Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs62490312	FASTK	cis	brain	BrainEAC
rs62490312	C7orf29	cis	brain	BrainEAC

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:150785000-150812000	Weak transcription	Aorta	Aorta
2	chr7:150786400-150808400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr7:150787200-150800600	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr7:150787200-150801400	Weak transcription	NH-A	brain
5	chr7:150787400-150807800	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr7:150787800-150801800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr7:150787800-150801800	Weak transcription	NHLF	lung
8	chr7:150788400-150800600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr7:150788600-150807400	Weak transcription	Fetal Heart	heart
10	chr7:150789000-150801400	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr7:150789000-150815400	Weak transcription	GM12878-XiMat	blood
12	chr7:150789200-150801600	Weak transcription	Colonic Mucosa	Colon
13	chr7:150789200-150802400	Strong transcription	Fetal Stomach	stomach
14	chr7:150789400-150801600	Weak transcription	Pancreas	Pancrea
15	chr7:150789400-150807800	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr7:150789600-150807000	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr7:150789800-150800600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr7:150789800-150806600	Weak transcription	Duodenum Mucosa	Duodenum
19	chr7:150790000-150801800	Weak transcription	Osteobl	bone
20	chr7:150790000-150803400	Weak transcription	Liver	Liver
21	chr7:150790400-150801600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr7:150790400-150806200	Weak transcription	Rectal Smooth Muscle	rectum
23	chr7:150792400-150800800	Weak transcription	HepG2	liver
24	chr7:150792400-150801000	Weak transcription	HUVEC	blood vessel
25	chr7:150792400-150801200	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr7:150792600-150805400	Weak transcription	A549	lung
27	chr7:150792600-150810200	Weak transcription	Esophagus	oesophagus
28	chr7:150793400-150801800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr7:150793400-150801800	Weak transcription	NHDF-Ad	bronchial
30	chr7:150793400-150805600	Weak transcription	Ovary	ovary
31	chr7:150793400-150808000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
32	chr7:150793600-150806600	Weak transcription	Placenta	Placenta
33	chr7:150794000-150808800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
34	chr7:150794200-150801000	Weak transcription	Fetal Intestine Large	intestine
35	chr7:150794800-150801600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr7:150794800-150807800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr7:150795000-150807800	Weak transcription	NHEK	skin
38	chr7:150796600-150801600	Enhancers	H1 Cell Line	embryonic stem cell
39	chr7:150797000-150806000	Weak transcription	Colon Smooth Muscle	Colon
40	chr7:150797000-150807800	Weak transcription	Fetal Lung	lung
41	chr7:150797000-150808400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr7:150797200-150801600	Weak transcription	HSMM	muscle
43	chr7:150797200-150801800	Weak transcription	HSMMtube	muscle
44	chr7:150797400-150801600	Weak transcription	Muscle Satellite Cultured Cells	--
45	chr7:150797400-150808000	Weak transcription	Rectal Mucosa Donor 31	rectum
46	chr7:150797400-150810200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr7:150797600-150800600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr7:150797600-150801000	Weak transcription	Lung	lung
49	chr7:150797600-150801600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr7:150797600-150802000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links