Variant report

Variant	rs6836128
Chromosome Location	chr4:87863770-87863771
allele	C/T
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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:87862443..87864681-chr4:87929416..87931168,2	MCF-7	breast:
2	chr4:87863295..87865719-chr4:87926718..87928690,2	MCF-7	breast:
3	chr4:87861846..87864713-chr4:88083470..88086069,2	K562	blood:
4	chr4:87854585..87857890-chr4:87861673..87864698,5	MCF-7	breast:
5	chr4:87821787..87824264-chr4:87863073..87865329,2	K562	blood:
6	chr4:87853595..87871697-chr4:87924007..87941983,77	K562	blood:
7	chr4:87861604..87864179-chr4:87870978..87873929,2	K562	blood:
8	chr4:87855630..87856280-chr4:87863253..87863945,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000235043	Chromatin interaction
ENSG00000163633	Chromatin interaction
ENSG00000172493	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs12506662	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1447993	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17012186	0.92[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs1868246	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1992876	0.88[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.88[ASN][1000 genomes]
rs2442078	0.85[EUR][1000 genomes]
rs2705621	0.94[CEU][hapmap];0.93[TSI][hapmap];0.92[EUR][1000 genomes]
rs28522052	0.85[ASN][1000 genomes]
rs2869632	0.92[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2904151	0.92[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs3775229	0.82[CHD][hapmap];0.87[JPT][hapmap]
rs3775230	0.86[CHD][hapmap];0.87[JPT][hapmap]
rs61586576	0.88[ASN][1000 genomes]
rs6419117	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs67773101	0.88[ASN][1000 genomes]
rs725030	0.92[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs72613148	0.92[EUR][1000 genomes]
rs72613149	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7657530	0.82[YRI][hapmap]
rs7671931	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7693780	0.81[ASN][1000 genomes]
rs7693889	0.85[ASN][1000 genomes]
rs9996533	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv594787	chr4:87221827-87888667	Enhancers Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv1013308	chr4:87769694-87870168	Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	nsv508297	chr4:87778783-87868508	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
4	nsv1009937	chr4:87795314-88008345	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6836128	HERC6	cis	cerebellum	SCAN

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:87857600-87882000	Weak transcription	Spleen	Spleen
2	chr4:87857800-87867800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr4:87857800-87880200	Weak transcription	HSMM	muscle
4	chr4:87858000-87867600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr4:87858200-87866800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr4:87858200-87869400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr4:87858600-87864800	Enhancers	Fetal Thymus	thymus
8	chr4:87858600-87881000	Weak transcription	Stomach Smooth Muscle	stomach
9	chr4:87858800-87864400	Enhancers	Liver	Liver
10	chr4:87859000-87864400	Enhancers	Fetal Intestine Large	intestine
11	chr4:87859200-87865600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr4:87859800-87864000	Enhancers	Skeletal Muscle Female	skeletal muscle
13	chr4:87861000-87864800	Enhancers	HepG2	liver
14	chr4:87861000-87878000	Weak transcription	HMEC	breast
15	chr4:87861200-87863800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
16	chr4:87861200-87863800	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr4:87861200-87864200	Enhancers	Rectal Mucosa Donor 31	rectum
18	chr4:87861200-87864400	Enhancers	HUVEC	blood vessel
19	chr4:87861200-87864800	Enhancers	Primary hematopoietic stem cells short term culture	blood
20	chr4:87861400-87864400	Enhancers	Rectal Mucosa Donor 29	rectum
21	chr4:87861400-87864800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr4:87861400-87865400	Weak transcription	HUES64 Cell Line	embryonic stem cell
23	chr4:87861400-87865800	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr4:87861400-87866200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr4:87861400-87866200	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr4:87861400-87867800	Weak transcription	Right Ventricle	heart
27	chr4:87861400-87868000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
28	chr4:87861400-87877200	Weak transcription	Placenta Amnion	Placenta Amnion
29	chr4:87861400-87880800	Weak transcription	Aorta	Aorta
30	chr4:87861600-87864600	Enhancers	Primary T helper cells PMA-I stimulated	--
31	chr4:87861600-87864600	Enhancers	Hela-S3	cervix
32	chr4:87861600-87864800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
33	chr4:87861600-87865600	Weak transcription	Left Ventricle	heart
34	chr4:87861600-87865800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr4:87861600-87868000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
36	chr4:87861600-87868000	Weak transcription	Fetal Lung	lung
37	chr4:87861600-87868000	Weak transcription	Skeletal Muscle Male	skeletal muscle
38	chr4:87861600-87868400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr4:87861600-87868400	Weak transcription	Brain Cingulate Gyrus	brain
40	chr4:87861600-87869200	Weak transcription	Brain Hippocampus Middle	brain
41	chr4:87861600-87870400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr4:87861800-87863800	Enhancers	Primary T cells from cord blood	blood
43	chr4:87861800-87863800	Weak transcription	Right Atrium	heart
44	chr4:87861800-87866000	Weak transcription	Fetal Heart	heart
45	chr4:87861800-87866000	Weak transcription	Monocytes-CD14+_RO01746	blood
46	chr4:87861800-87867800	Weak transcription	Esophagus	oesophagus
47	chr4:87861800-87868000	Weak transcription	Colonic Mucosa	Colon
48	chr4:87861800-87868200	Weak transcription	Adipose Nuclei	Adipose
49	chr4:87861800-87871600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr4:87861800-87871600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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