Variant report

Variant	rs71569399
Chromosome Location	chr6:37959542-37959543
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:37948324..37950868-chr6:37959290..37962178,2	MCF-7	breast:
2	chr6:37959253..37960891-chr6:37963216..37966169,3	K562	blood:
3	chr6:37956692..37960891-chr6:37962737..37966006,6	K562	blood:

Extended variants
information (count: 65 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs13195333	0.81[AFR][1000 genomes]
rs13198459	0.83[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs13200310	0.87[AMR][1000 genomes]
rs13203867	0.85[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs13210087	0.93[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs13210967	0.87[AMR][1000 genomes]
rs13212369	0.84[EUR][1000 genomes]
rs13217630	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13219500	0.83[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs16890301	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2395689	0.82[EUR][1000 genomes]
rs2645104	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2645115	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2645118	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2645121	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2645123	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2645126	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28385568	0.81[AFR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2842498	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2842524	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs33997846	0.94[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs34038972	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs34123707	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34406273	0.88[EUR][1000 genomes]
rs34449592	0.89[AFR][1000 genomes]
rs34618835	0.83[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs34634043	0.86[AFR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs34754573	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35051126	0.82[EUR][1000 genomes]
rs35202194	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35379375	0.87[AMR][1000 genomes]
rs35465740	0.86[AFR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs35575717	0.86[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs35597126	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs35815938	0.84[EUR][1000 genomes]
rs35955196	0.82[AFR][1000 genomes]
rs4394213	0.86[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs55943813	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56678832	0.82[EUR][1000 genomes]
rs6458037	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6908761	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6916057	0.84[EUR][1000 genomes]
rs6916535	0.80[ASN][1000 genomes]
rs6917208	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6917736	0.86[AFR][1000 genomes]
rs6923132	0.86[AFR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6923254	0.86[AFR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6923665	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6925563	0.86[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs6940491	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs71569397	0.86[AFR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs71569402	0.82[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs71571304	0.84[EUR][1000 genomes]
rs7740636	0.88[EUR][1000 genomes]
rs7757560	0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7776025	0.86[AFR][1000 genomes];0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1028825	chr6:37495154-38278320	Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv1024016	chr6:37567651-37981590	Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv1017051	chr6:37789341-38084719	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv538203	chr6:37789341-38084719	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv1018711	chr6:37813397-37981590	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv1020625	chr6:37833591-38155622	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
7	nsv1021991	chr6:37893949-38738720	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
8	nsv602956	chr6:37909084-37986489	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	esv2761037	chr6:37930659-37966762	Weak transcription Enhancers ZNF genes & repeats Genic enhancers Strong transcription Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:37949800-37962000	Weak transcription	Small Intestine	intestine
2	chr6:37950000-37963600	Weak transcription	Spleen	Spleen
3	chr6:37951800-37959800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr6:37952200-37961400	Enhancers	Liver	Liver
5	chr6:37953400-37960400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr6:37953400-37962600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr6:37953400-37962600	Weak transcription	Lung	lung
8	chr6:37953400-37965200	Weak transcription	Esophagus	oesophagus
9	chr6:37954000-37959600	Enhancers	HSMMtube	muscle
10	chr6:37954000-37960200	Enhancers	Colon Smooth Muscle	Colon
11	chr6:37954000-37960600	Enhancers	HSMM	muscle
12	chr6:37954200-37963000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr6:37954400-37960200	Enhancers	Muscle Satellite Cultured Cells	--
14	chr6:37954600-37960200	Enhancers	NHLF	lung
15	chr6:37955400-37959600	Enhancers	Brain Substantia Nigra	brain
16	chr6:37955400-37959600	Enhancers	Skeletal Muscle Female	skeletal muscle
17	chr6:37955400-37960400	Enhancers	Adipose Nuclei	Adipose
18	chr6:37955400-37960400	Enhancers	Skeletal Muscle Male	skeletal muscle
19	chr6:37955400-37960400	Enhancers	Stomach Smooth Muscle	stomach
20	chr6:37955400-37960800	Enhancers	Rectal Smooth Muscle	rectum
21	chr6:37955600-37960000	Enhancers	NHDF-Ad	bronchial
22	chr6:37955600-37963800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr6:37956200-37961800	Weak transcription	Fetal Brain Female	brain
24	chr6:37956200-37962000	Weak transcription	Fetal Stomach	stomach
25	chr6:37956200-37965400	Weak transcription	Primary hematopoietic stem cells	blood
26	chr6:37956200-37978800	Weak transcription	Primary T cells from cord blood	blood
27	chr6:37956400-37960200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
28	chr6:37956400-37961400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr6:37956600-37961800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr6:37956600-37961800	Weak transcription	Pancreatic Islets	Pancreatic Islet
31	chr6:37956600-37962000	Weak transcription	Brain Angular Gyrus	brain
32	chr6:37956600-37962000	Weak transcription	Fetal Kidney	kidney
33	chr6:37956600-37967200	Weak transcription	Primary B cells from cord blood	blood
34	chr6:37956800-37960200	Enhancers	GM12878-XiMat	blood
35	chr6:37956800-37961600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
36	chr6:37956800-37962000	Weak transcription	Brain Cingulate Gyrus	brain
37	chr6:37957600-37960400	Enhancers	Cortex derived primary cultured neurospheres	brain
38	chr6:37957600-37961800	Weak transcription	Brain Germinal Matrix	brain
39	chr6:37957600-37962200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr6:37957600-37962400	Weak transcription	Pancreas	Pancrea
41	chr6:37957800-37959600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr6:37957800-37959600	Enhancers	NHEK	skin
43	chr6:37957800-37960200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr6:37957800-37960600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr6:37957800-37961600	Weak transcription	Brain Inferior Temporal Lobe	brain
46	chr6:37957800-37962200	Weak transcription	Fetal Brain Male	brain
47	chr6:37957800-37976400	Weak transcription	Aorta	Aorta
48	chr6:37958000-37959600	Enhancers	Osteobl	bone
49	chr6:37958000-37960400	Enhancers	Duodenum Smooth Muscle	Duodenum
50	chr6:37958000-37961600	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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