Variant report

Variant	rs2904151
Chromosome Location	chr4:87888667-87888668
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:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:87875765..87890159-chr4:87922878..87933002,25	K562	blood:
2	chr4:87885535..87895894-chr4:87923652..87929924,15	K562	blood:
3	chr4:87876506..87878557-chr4:87886269..87888945,2	K562	blood:
4	chr4:87856231..87859269-chr4:87886657..87889990,3	K562	blood:
5	chr4:87881072..87882876-chr4:87886883..87888744,2	MCF-7	breast:
6	chr4:87881202..87884789-chr4:87884979..87890767,11	K562	blood:
7	chr4:87887515..87891253-chr4:87896887..87898835,3	MCF-7	breast:
8	chr4:87887576..87890544-chr4:87927367..87929532,2	MCF-7	breast:
9	chr4:87885045..87886617-chr4:87888057..87889628,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000163633	Chromatin interaction
ENSG00000172493	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs12506662	0.86[ASN][1000 genomes]
rs1447993	0.92[CHB][hapmap];0.89[CHD][hapmap]
rs17012186	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1868246	0.92[CHB][hapmap];0.89[CHD][hapmap];0.92[MEX][hapmap]
rs1992876	0.81[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.96[ASN][1000 genomes]
rs28522052	0.99[ASN][1000 genomes]
rs2869632	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3775229	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]
rs3775230	0.81[CEU][hapmap];0.85[CHB][hapmap];0.96[CHD][hapmap];0.87[JPT][hapmap]
rs386485	0.81[AFR][1000 genomes]
rs61586576	0.96[ASN][1000 genomes]
rs67773101	0.96[ASN][1000 genomes]
rs6836128	0.92[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs725030	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7671931	0.86[ASN][1000 genomes]
rs7693780	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7693889	0.99[ASN][1000 genomes]
rs9996533	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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	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
3	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
4	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
5	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
6	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
7	nsv291773	chr4:87884343-87891031	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2904151	KLHL8	cis	cerebellum	SCAN
rs2904151	PKD2	cis	parietal	SCAN
rs2904151	HERC6	cis	cerebellum	SCAN

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:87868400-87891800	Weak transcription	Esophagus	oesophagus
2	chr4:87868600-87898000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr4:87869800-87894000	Weak transcription	Brain Cingulate Gyrus	brain
4	chr4:87872600-87926200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr4:87872800-87891400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr4:87878800-87891600	Weak transcription	NHEK	skin
7	chr4:87881000-87891800	Weak transcription	Lung	lung
8	chr4:87881000-87897600	Weak transcription	Brain Angular Gyrus	brain
9	chr4:87881200-87890000	Weak transcription	Aorta	Aorta
10	chr4:87882000-87895400	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr4:87882200-87889800	Weak transcription	Pancreas	Pancrea
12	chr4:87882200-87891400	Weak transcription	Ovary	ovary
13	chr4:87882200-87895600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr4:87882400-87893800	Weak transcription	Colonic Mucosa	Colon
15	chr4:87882400-87898600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr4:87882600-87891400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr4:87882600-87920200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr4:87882800-87889600	Weak transcription	Small Intestine	intestine
19	chr4:87882800-87891600	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr4:87882800-87912400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr4:87883000-87889200	Weak transcription	Left Ventricle	heart
22	chr4:87883000-87889800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr4:87883000-87889800	Weak transcription	Psoas Muscle	Psoas
24	chr4:87883000-87891800	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr4:87883200-87889200	Weak transcription	Adipose Nuclei	Adipose
26	chr4:87883400-87889600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr4:87883800-87890600	Enhancers	Fetal Thymus	thymus
28	chr4:87883800-87891800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr4:87883800-87891800	Weak transcription	Fetal Intestine Large	intestine
30	chr4:87883800-87894200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr4:87884200-87893800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr4:87884200-87894000	Weak transcription	Fetal Intestine Small	intestine
33	chr4:87885000-87891400	Weak transcription	Stomach Mucosa	stomach
34	chr4:87885000-87891800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr4:87885000-87894200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr4:87885000-87894200	Weak transcription	HMEC	breast
37	chr4:87885400-87889800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr4:87885800-87889800	Enhancers	K562	blood
39	chr4:87885800-87890000	Enhancers	Primary B cells from cord blood	blood
40	chr4:87885800-87890200	Enhancers	Primary B cells from peripheral blood	blood
41	chr4:87885800-87890600	Enhancers	Primary hematopoietic stem cells short term culture	blood
42	chr4:87886000-87889200	Enhancers	HUES6 Cell Line	embryonic stem cell
43	chr4:87886000-87889800	Enhancers	iPS-15b Cell Line	embryonic stem cell
44	chr4:87886000-87889800	Enhancers	Primary monocytes fromperipheralblood	blood
45	chr4:87886000-87890000	Enhancers	HUES48 Cell Line	embryonic stem cell
46	chr4:87886000-87890400	Enhancers	Thymus	Thymus
47	chr4:87886400-87890000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
48	chr4:87886400-87890200	Enhancers	H1 Cell Line	embryonic stem cell
49	chr4:87886400-87890600	Genic enhancers	Placenta	Placenta
50	chr4:87886600-87889200	Weak transcription	A549	lung

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