Variant report

Variant	rs28745897
Chromosome Location	chr6:31717066-31717067
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:31717061-31717083	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:31715039..31718016-chr6:31863817..31867579,3	K562	blood:
2	chr6:31712086..31714995-chr6:31716083..31718162,2	MCF-7	breast:

Variant related genes	Relation type
MSH5	TF binding region
ENSG00000204410	Chromatin interaction
ENSG00000166278	Chromatin interaction
ENSG00000204371	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs17201144	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34406901	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34431565	0.87[AMR][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	nsv601609	chr6:31280101-31799786	Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Enhancers Genic enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	332 gene(s)	inside rSNPs	diseases
2	nsv601610	chr6:31280101-31960770	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	370 gene(s)	inside rSNPs	diseases
3	nsv601628	chr6:31280327-31990098	Weak transcription Transcr. at gene 5' and 3' Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	376 gene(s)	inside rSNPs	diseases
4	nsv601629	chr6:31280327-31996185	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	376 gene(s)	inside rSNPs	diseases
5	nsv601630	chr6:31280327-32011317	Genic enhancers Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS 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 miRNA target site	378 gene(s)	inside rSNPs	diseases
6	nsv601631	chr6:31280327-32017540	Genic enhancers Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	378 gene(s)	inside rSNPs	diseases
7	nsv1023939	chr6:31325961-32026747	Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	372 gene(s)	inside rSNPs	diseases
8	nsv538188	chr6:31325961-32026747	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	372 gene(s)	inside rSNPs	diseases
9	nsv432868	chr6:31338844-31721033	Bivalent/Poised TSS Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	250 gene(s)	inside rSNPs	diseases
10	nsv1021747	chr6:31386219-31907266	Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	330 gene(s)	inside rSNPs	diseases
11	nsv884418	chr6:31525448-31741078	Active TSS Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	206 gene(s)	inside rSNPs	diseases
12	nsv1033154	chr6:31550614-32009410	Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	326 gene(s)	inside rSNPs	diseases
13	nsv1017945	chr6:31609641-32481240	Genic enhancers Weak transcription Transcr. at gene 5' and 3' Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
14	esv3428142	chr6:31615800-31881809	Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	257 gene(s)	inside rSNPs	diseases
15	nsv819978	chr6:31713259-31721119	Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
16	esv2763547	chr6:31715882-31738478	Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:31707400-31724600	Weak transcription	Fetal Heart	heart
2	chr6:31708200-31733800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr6:31708400-31717600	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr6:31708400-31727000	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr6:31708400-31729600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr6:31708400-31731000	Weak transcription	HSMMtube	muscle
7	chr6:31708400-31731200	Weak transcription	Gastric	stomach
8	chr6:31708400-31731200	Weak transcription	Lung	lung
9	chr6:31708400-31731200	Weak transcription	Right Atrium	heart
10	chr6:31708600-31728200	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr6:31708600-31729400	Weak transcription	Fetal Lung	lung
12	chr6:31708600-31731200	Weak transcription	Brain Hippocampus Middle	brain
13	chr6:31708600-31732000	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr6:31708600-31734400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr6:31708800-31723200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr6:31708800-31727400	Weak transcription	Primary T cells fromperipheralblood	blood
17	chr6:31708800-31727600	Weak transcription	Spleen	Spleen
18	chr6:31708800-31731200	Weak transcription	Brain Anterior Caudate	brain
19	chr6:31708800-31737400	Weak transcription	Liver	Liver
20	chr6:31709000-31718200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr6:31709000-31719000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr6:31709000-31720400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr6:31709000-31720400	Weak transcription	NH-A	brain
24	chr6:31709000-31720400	Weak transcription	NHDF-Ad	bronchial
25	chr6:31709000-31721000	Weak transcription	Brain Substantia Nigra	brain
26	chr6:31709000-31722400	Weak transcription	Fetal Brain Male	brain
27	chr6:31709000-31726800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
28	chr6:31709000-31727000	Weak transcription	Primary T cells from cord blood	blood
29	chr6:31709000-31727600	Weak transcription	Colonic Mucosa	Colon
30	chr6:31709000-31738200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr6:31709200-31727200	Weak transcription	Brain Germinal Matrix	brain
32	chr6:31709200-31728400	Weak transcription	Stomach Mucosa	stomach
33	chr6:31709200-31737400	Weak transcription	Primary B cells from peripheral blood	blood
34	chr6:31709600-31727800	Weak transcription	Hela-S3	cervix
35	chr6:31709600-31737400	Weak transcription	Rectal Mucosa Donor 31	rectum
36	chr6:31709800-31718000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr6:31709800-31727200	Weak transcription	Primary neutrophils fromperipheralblood	blood
38	chr6:31710000-31731000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
39	chr6:31710600-31731200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
40	chr6:31710800-31720400	Weak transcription	Muscle Satellite Cultured Cells	--
41	chr6:31710800-31726400	Weak transcription	Primary hematopoietic stem cells	blood
42	chr6:31710800-31731000	Weak transcription	HUVEC	blood vessel
43	chr6:31711200-31718600	Strong transcription	Dnd41	blood
44	chr6:31711200-31727600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
45	chr6:31711200-31731400	Weak transcription	Fetal Kidney	kidney
46	chr6:31711400-31726600	Weak transcription	Primary B cells from cord blood	blood
47	chr6:31712000-31726800	Weak transcription	Primary monocytes fromperipheralblood	blood
48	chr6:31712200-31728000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
49	chr6:31712400-31718200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr6:31713800-31717400	Strong transcription	Fetal Intestine Small	intestine

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links