Variant report

Variant	rs3775229
Chromosome Location	chr4:87978626-87978627
allele	G/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	chr4:87977551..87981344-chr4:87982047..87984756,4	K562	blood:
2	chr4:87973947..87977443-chr4:87977698..87982276,5	K562	blood:
3	chr4:87926976..87930331-chr4:87978377..87981328,6	K562	blood:
4	chr4:87925846..87930633-chr4:87974014..87981325,14	K562	blood:
5	chr4:87931438..87933105-chr4:87978302..87980723,2	K562	blood:
6	chr4:87927271..87930091-chr4:87977611..87979690,2	MCF-7	breast:
7	chr4:87928043..87929592-chr4:87976767..87978738,2	MCF-7	breast:
8	chr4:87853906..87856059-chr4:87978530..87982549,4	K562	blood:

No data

Variant related genes	Relation type
ENSG00000163633	Chromatin interaction
ENSG00000172493	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs1447993	0.82[CHD][hapmap]
rs17012186	0.85[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs1868246	0.82[CHD][hapmap]
rs1992876	0.93[CHD][hapmap];0.87[JPT][hapmap]
rs2869632	0.85[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs2904151	0.85[CHB][hapmap];0.93[CHD][hapmap];0.87[JPT][hapmap];1.00[LWK][hapmap];0.93[MKK][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs3755979	0.85[CHB][hapmap]
rs3775230	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs386485	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6836128	0.82[CHD][hapmap];0.87[JPT][hapmap]
rs725030	0.85[CHB][hapmap];0.93[CHD][hapmap];0.87[JPT][hapmap];0.93[MKK][hapmap];1.00[YRI][hapmap];0.81[AFR][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	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
2	nsv999176	chr4:87869996-88098136	Strong transcription Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	nsv998335	chr4:87869996-88104414	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv1001017	chr4:87872160-88087003	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
5	nsv537166	chr4:87872160-88087003	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
6	nsv999098	chr4:87899091-88016048	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
7	nsv537167	chr4:87899091-88016048	Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
8	nsv997750	chr4:87933945-88264127	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
9	nsv879525	chr4:87964363-88033352	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3775229	HERC6	cis	cerebellum	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:87961000-87979200	Weak transcription	HSMMtube	muscle
2	chr4:87963200-87982200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr4:87964600-87995000	Weak transcription	Hela-S3	cervix
4	chr4:87964800-87979200	Weak transcription	A549	lung
5	chr4:87966200-87979200	Weak transcription	NH-A	brain
6	chr4:87968600-87979000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr4:87968800-87978800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
8	chr4:87968800-87979000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr4:87968800-87979200	Weak transcription	HMEC	breast
10	chr4:87968800-87979200	Weak transcription	HSMM	muscle
11	chr4:87968800-87979400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr4:87968800-87979400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr4:87968800-87980000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr4:87968800-87982000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr4:87968800-87982200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr4:87968800-87983400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr4:87968800-87995000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr4:87969000-87994600	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr4:87970200-87979200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
20	chr4:87970200-87979800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr4:87970200-87989800	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr4:87970400-87982200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr4:87971400-87979400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr4:87972200-87979800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr4:87972200-87982200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr4:87972400-87982200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr4:87972600-87980400	Weak transcription	Primary T cells from cord blood	blood
28	chr4:87973800-87980200	Enhancers	Liver	Liver
29	chr4:87973800-87980200	Enhancers	Rectal Mucosa Donor 31	rectum
30	chr4:87974800-87981200	Enhancers	HUES64 Cell Line	embryonic stem cell
31	chr4:87975000-87979800	Weak transcription	Pancreatic Islets	Pancreatic Islet
32	chr4:87975000-87987800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr4:87975200-87979400	Weak transcription	H1 Cell Line	embryonic stem cell
34	chr4:87975200-87979800	Enhancers	Rectal Smooth Muscle	rectum
35	chr4:87975400-87981200	Enhancers	Fetal Intestine Large	intestine
36	chr4:87975600-87979200	Enhancers	Fetal Intestine Small	intestine
37	chr4:87975800-87979200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr4:87976000-87979000	Weak transcription	Stomach Mucosa	stomach
39	chr4:87976000-87979200	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr4:87976000-87979200	Weak transcription	Thymus	Thymus
41	chr4:87976000-87979400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
42	chr4:87976200-87979200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr4:87976200-87979200	Weak transcription	NHEK	skin
44	chr4:87976200-87979600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr4:87976200-87989800	Weak transcription	Fetal Muscle Trunk	muscle
46	chr4:87976400-87979200	Weak transcription	HUES6 Cell Line	embryonic stem cell
47	chr4:87976400-87979200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr4:87976400-87979200	Weak transcription	Esophagus	oesophagus
49	chr4:87976400-87979400	Weak transcription	Primary T cells fromperipheralblood	blood
50	chr4:87976400-87979400	Weak transcription	Gastric	stomach

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