Variant report

Variant	rs3798539
Chromosome Location	chr6:34209844-34209845
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:19)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:19 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:34209557..34211500-chr6:34382347..34384028,2	K562	blood:
2	chr10:57012609..57015608-chr6:34209555..34212466,2	K562	blood:
3	chr12:110866419..110868618-chr6:34208712..34210683,2	K562	blood:
4	chr6:34209691..34211647-chr6:34293997..34295564,2	K562	blood:
5	chr6:34209711..34212702-chr6:34323551..34325393,2	MCF-7	breast:
6	chr6:34191465..34193341-chr6:34208084..34210074,2	MCF-7	breast:
7	chr6:34209391..34211783-chr6:34743320..34745322,2	K562	blood:
8	chr6:34209668..34211414-chr6:34604558..34606147,2	K562	blood:
9	chr6:34094743..34096794-chr6:34209207..34210830,2	K562	blood:
10	chr6:34149535..34152923-chr6:34209211..34212151,3	K562	blood:
11	chr6:34209103..34211668-chr6:34357730..34361884,5	K562	blood:
12	chr6:34208449..34211320-chr6:34575823..34577812,2	K562	blood:
13	chr6:34112613..34114154-chr6:34208164..34210617,2	K562	blood:
14	chr6:34209704..34212445-chr6:34360073..34361578,2	MCF-7	breast:
15	chr6:34208090..34210823-chr6:34391243..34393552,2	K562	blood:
16	chr6:34202383..34217863-chr6:34357259..34364960,37	K562	blood:
17	chr6:34209005..34211629-chr6:34285678..34287201,2	K562	blood:
18	chr6:34143529..34145401-chr6:34209806..34212662,2	K562	blood:
19	chr6:34209798..34218235-chr6:34387971..34396103,20	K562	blood:

No data

Variant related genes	Relation type
ENSG00000270800	Chromatin interaction
ENSG00000124614	Chromatin interaction
ENSG00000258011	Chromatin interaction
ENSG00000124493	Chromatin interaction
ENSG00000272325	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs11963724	1.00[CHB][hapmap];1.00[EUR][1000 genomes]
rs11966568	1.00[CHB][hapmap]
rs13214721	1.00[CHB][hapmap]
rs28405247	0.92[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6922119	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs9461967	0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv432881	chr6:34026522-34213822	Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv885781	chr6:34110257-34247661	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers 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	56 gene(s)	inside rSNPs	diseases
3	nsv462903	chr6:34110257-34263743	Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
4	nsv602863	chr6:34110257-34263743	Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
5	nsv885783	chr6:34187206-34209844	Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
6	nsv885784	chr6:34187206-34246714	Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
7	nsv602865	chr6:34203406-34217181	Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
8	esv1798756	chr6:34203406-34319041	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
9	esv1798835	chr6:34204183-34319041	Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
10	esv1840881	chr6:34204285-34231570	Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Weak transcription 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	47 gene(s)	inside rSNPs	diseases
11	esv1792088	chr6:34204285-34318837	Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
12	esv1793127	chr6:34204285-34319041	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:34205400-34216600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr6:34206000-34212000	Weak transcription	Ovary	ovary
3	chr6:34206200-34212600	Weak transcription	Aorta	Aorta
4	chr6:34206400-34210000	Weak transcription	HSMMtube	muscle
5	chr6:34206400-34210600	Weak transcription	Right Atrium	heart
6	chr6:34206400-34211600	Weak transcription	Colon Smooth Muscle	Colon
7	chr6:34206400-34211600	Weak transcription	Left Ventricle	heart
8	chr6:34206400-34215800	Weak transcription	Rectal Smooth Muscle	rectum
9	chr6:34206400-34216000	Weak transcription	Fetal Kidney	kidney
10	chr6:34206400-34216000	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr6:34206800-34210200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr6:34206800-34210600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr6:34207000-34210600	Weak transcription	Small Intestine	intestine
14	chr6:34207000-34212000	Weak transcription	Psoas Muscle	Psoas
15	chr6:34207000-34212600	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
16	chr6:34207200-34210800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr6:34207200-34215000	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr6:34207400-34210000	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr6:34207400-34210800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr6:34207400-34211600	Transcr. at gene 5' and 3'	Hela-S3	cervix
21	chr6:34207600-34210200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr6:34207600-34210800	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr6:34207600-34212200	Transcr. at gene 5' and 3'	Breast Myoepithelial Primary Cells	Breast
24	chr6:34207600-34212400	Genic enhancers	Fetal Thymus	thymus
25	chr6:34207600-34213600	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr6:34207600-34216600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr6:34207800-34210400	Genic enhancers	Muscle Satellite Cultured Cells	--
28	chr6:34207800-34210600	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
29	chr6:34207800-34210800	Genic enhancers	HMEC	breast
30	chr6:34207800-34211600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr6:34207800-34215000	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr6:34207800-34215600	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr6:34207800-34215800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr6:34208000-34210800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr6:34208000-34211600	Weak transcription	Stomach Mucosa	stomach
36	chr6:34208200-34210000	Genic enhancers	NHEK	skin
37	chr6:34208200-34210200	Strong transcription	H9 Cell Line	embryonic stem cell
38	chr6:34208200-34210200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr6:34208200-34210600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr6:34208200-34210600	Genic enhancers	HUVEC	blood vessel
41	chr6:34208200-34211000	Strong transcription	Placenta Amnion	Placenta Amnion
42	chr6:34208200-34211000	Strong transcription	Spleen	Spleen
43	chr6:34208200-34211400	Genic enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr6:34208200-34211400	Strong transcription	Primary monocytes fromperipheralblood	blood
45	chr6:34208200-34212000	Strong transcription	Fetal Muscle Trunk	muscle
46	chr6:34208200-34212000	Genic enhancers	NHLF	lung
47	chr6:34208200-34212600	Genic enhancers	H1 Cell Line	embryonic stem cell
48	chr6:34208200-34214200	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
49	chr6:34208400-34210400	Genic enhancers	A549	lung
50	chr6:34208400-34210800	Strong transcription	Esophagus	oesophagus

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