Variant report

Variant	rs3901371
Chromosome Location	chr7:50700936-50700937
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:50535443..50536367-chr7:50700303..50701436,9	MCF-7	breast:
2	chr7:50535602..50536304-chr7:50700570..50701281,2	K562	blood:
3	chr7:50699706..50701584-chr7:50708525..50710076,2	K562	blood:
4	chr7:50697685..50701045-chr7:50715068..50717759,3	K562	blood:

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10261940	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11238265	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11575319	1.00[YRI][hapmap]
rs12530592	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17133918	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17133922	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2190495	1.00[CHB][hapmap]
rs2237442	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2237448	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2237452	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2237455	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2237457	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2237460	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2237462	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2237465	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2237467	0.94[ASN][1000 genomes]
rs2237468	0.83[ASN][1000 genomes]
rs2237471	0.87[CHB][hapmap]
rs2244347	0.86[CHB][hapmap]
rs2282926	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2282927	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2282928	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2282929	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3807547	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3819432	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4504586	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs58587127	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6593077	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs737292	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7792550	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7792811	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7797159	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs886822	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs886823	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9886137	0.89[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	nsv1016665	chr7:50452552-51404524	Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv1015758	chr7:50565404-50768153	Flanking Active TSS Genic enhancers Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
3	nsv1023228	chr7:50573214-50777634	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
4	nsv1032882	chr7:50611138-50775257	Genic enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
5	nsv538834	chr7:50611138-50775257	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
6	nsv1031138	chr7:50651793-50814881	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:50674200-50709800	Weak transcription	Esophagus	oesophagus
2	chr7:50682600-50704600	Weak transcription	Primary hematopoietic stem cells	blood
3	chr7:50693600-50705400	Weak transcription	NH-A	brain
4	chr7:50694200-50729200	Weak transcription	Hela-S3	cervix
5	chr7:50694600-50707800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr7:50694600-50708400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr7:50694800-50701000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr7:50695000-50701000	Enhancers	Left Ventricle	heart
9	chr7:50695000-50720600	Weak transcription	Primary T cells from cord blood	blood
10	chr7:50695600-50716000	Weak transcription	Fetal Stomach	stomach
11	chr7:50695800-50701000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr7:50697600-50716600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr7:50697800-50716800	Weak transcription	Stomach Smooth Muscle	stomach
14	chr7:50698200-50708800	Weak transcription	HSMMtube	muscle
15	chr7:50698600-50701000	Enhancers	Cortex derived primary cultured neurospheres	brain
16	chr7:50698800-50701000	Enhancers	Right Ventricle	heart
17	chr7:50699000-50701200	Enhancers	Liver	Liver
18	chr7:50699200-50701000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr7:50699200-50701000	Enhancers	Small Intestine	intestine
20	chr7:50699400-50701000	Enhancers	H1 Cell Line	embryonic stem cell
21	chr7:50699400-50701000	Enhancers	Duodenum Mucosa	Duodenum
22	chr7:50699400-50701200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
23	chr7:50699400-50701200	Enhancers	Stomach Mucosa	stomach
24	chr7:50699600-50701200	Enhancers	Skeletal Muscle Female	skeletal muscle
25	chr7:50699600-50702200	Weak transcription	Fetal Muscle Leg	muscle
26	chr7:50699600-50707800	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr7:50699600-50720400	Weak transcription	Colon Smooth Muscle	Colon
28	chr7:50699800-50701000	Enhancers	Sigmoid Colon	Sigmoid Colon
29	chr7:50700000-50701000	Enhancers	ES-I3 Cell Line	embryonic stem cell
30	chr7:50700000-50701000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr7:50700000-50701000	Enhancers	iPS-15b Cell Line	embryonic stem cell
32	chr7:50700000-50701000	Enhancers	Placenta	Placenta
33	chr7:50700000-50701200	Enhancers	HUES64 Cell Line	embryonic stem cell
34	chr7:50700200-50701200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr7:50700200-50701200	Enhancers	HUES48 Cell Line	embryonic stem cell
36	chr7:50700200-50701200	Enhancers	Placenta Amnion	Placenta Amnion
37	chr7:50700400-50701000	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr7:50700400-50701000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
39	chr7:50700400-50701000	Enhancers	Muscle Satellite Cultured Cells	--
40	chr7:50700400-50701000	Enhancers	Ovary	ovary
41	chr7:50700400-50701000	Enhancers	Pancreas	Pancrea
42	chr7:50700400-50701000	Enhancers	A549	lung
43	chr7:50700400-50701000	Enhancers	HSMM	muscle
44	chr7:50700400-50701200	Enhancers	HUVEC	blood vessel
45	chr7:50700600-50701000	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
46	chr7:50700600-50701000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr7:50700600-50701000	Enhancers	Brain Anterior Caudate	brain
48	chr7:50700600-50701000	Enhancers	Fetal Thymus	thymus
49	chr7:50700600-50701000	Enhancers	GM12878-XiMat	blood
50	chr7:50700600-50701000	Enhancers	HMEC	breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links