Variant report

Variant	rs62397007
Chromosome Location	chr6:38178403-38178404
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:38178185..38180709-chr6:38183811..38185746,2	K562	blood:

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10484933	0.92[ASN][1000 genomes]
rs10947720	0.90[ASN][1000 genomes]
rs12524219	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs12526138	1.00[AFR][1000 genomes]
rs12529300	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs12529640	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16890465	0.90[ASN][1000 genomes]
rs16890468	0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs16890511	0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs16890522	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs4711526	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4711530	1.00[AFR][1000 genomes]
rs4714127	1.00[AFR][1000 genomes]
rs4714135	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4714137	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4714142	1.00[AFR][1000 genomes]
rs62397004	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62397011	0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs62397015	1.00[AFR][1000 genomes]
rs6929505	0.94[ASN][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	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
3	nsv885817	chr6:38036420-39019503	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	nsv534620	chr6:38049585-38602064	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
5	nsv522522	chr6:38131442-38207636	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases
6	nsv885818	chr6:38147745-38436317	Enhancers Weak transcription Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv885819	chr6:38148770-38190439	Flanking Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv520053	chr6:38154941-38207636	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	nsv885820	chr6:38166511-38468887	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:38147400-38180400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr6:38160600-38179600	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr6:38160800-38201400	Weak transcription	Primary B cells from peripheral blood	blood
4	chr6:38162000-38179800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr6:38162600-38180000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr6:38166800-38194800	Weak transcription	Primary B cells from cord blood	blood
7	chr6:38167000-38210400	Weak transcription	Primary T cells from cord blood	blood
8	chr6:38174200-38180200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr6:38175400-38179600	Weak transcription	Psoas Muscle	Psoas
10	chr6:38175400-38180000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr6:38175800-38178800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr6:38176000-38179600	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr6:38176000-38184800	Enhancers	Fetal Muscle Leg	muscle
14	chr6:38176200-38181400	Enhancers	Fetal Stomach	stomach
15	chr6:38176800-38178800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
16	chr6:38176800-38179800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr6:38177000-38178600	Enhancers	Cortex derived primary cultured neurospheres	brain
18	chr6:38177000-38178800	Enhancers	Fetal Lung	lung
19	chr6:38177200-38178600	Enhancers	Brain Hippocampus Middle	brain
20	chr6:38177200-38178800	Enhancers	Ovary	ovary
21	chr6:38177200-38179000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr6:38177200-38179800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr6:38177400-38178800	Flanking Active TSS	Brain Germinal Matrix	brain
24	chr6:38177400-38178800	Enhancers	Brain Inferior Temporal Lobe	brain
25	chr6:38177400-38179000	Enhancers	Brain Cingulate Gyrus	brain
26	chr6:38177400-38179000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
27	chr6:38177400-38179000	Enhancers	Brain Substantia Nigra	brain
28	chr6:38177600-38178800	Enhancers	Primary T helper cells PMA-I stimulated	--
29	chr6:38177600-38180200	Weak transcription	Fetal Intestine Small	intestine
30	chr6:38177600-38189200	Weak transcription	Gastric	stomach
31	chr6:38177800-38178600	Enhancers	Brain Anterior Caudate	brain
32	chr6:38177800-38179600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr6:38177800-38179600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr6:38177800-38179600	Weak transcription	Spleen	Spleen
35	chr6:38177800-38179800	Weak transcription	Fetal Muscle Trunk	muscle
36	chr6:38177800-38180000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr6:38177800-38180000	Weak transcription	Rectal Smooth Muscle	rectum
38	chr6:38178000-38179600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
39	chr6:38178000-38180000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr6:38178000-38221600	Weak transcription	Primary T cells fromperipheralblood	blood
41	chr6:38178000-38221800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
42	chr6:38178200-38178600	Enhancers	Brain Angular Gyrus	brain
43	chr6:38178200-38179800	Weak transcription	HUES48 Cell Line	embryonic stem cell
44	chr6:38178200-38179800	Weak transcription	HUES64 Cell Line	embryonic stem cell
45	chr6:38178400-38178800	Enhancers	Fetal Brain Male	brain
46	chr6:38178400-38179000	Enhancers	Fetal Brain Female	brain
47	chr6:38178400-38179400	Weak transcription	Colon Smooth Muscle	Colon
48	chr6:38178400-38179600	Weak transcription	HUES6 Cell Line	embryonic stem cell
49	chr6:38178400-38179600	Weak transcription	Lung	lung
50	chr6:38178400-38179800	Weak transcription	Esophagus	oesophagus

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