Variant report

Variant	rs17012341
Chromosome Location	chr4:87983116-87983117
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:87980531..87986351-chr4:87988282..87991075,4	K562	blood:
2	chr4:87979844..87982158-chr4:87983072..87985121,2	K562	blood:
3	chr4:87926404..87928597-chr4:87982791..87984902,2	K562	blood:
4	chr4:87980531..87984297-chr4:87985969..87990791,4	K562	blood:
5	chr4:87977551..87981344-chr4:87982047..87984756,4	K562	blood:

Variant related genes	Relation type
ENSG00000172493	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10006308	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10010932	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10021180	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10021879	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10028134	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10032200	0.87[GIH][hapmap]
rs10489045	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17012304	0.87[GIH][hapmap]
rs17012361	1.00[JPT][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs189333	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs236988	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs236989	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs236990	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2904154	1.00[CEU][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs342455	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57516814	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72877982	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9995808	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][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

No data

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:87964600-87995000	Weak transcription	Hela-S3	cervix
2	chr4:87968800-87983400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr4:87968800-87995000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr4:87969000-87994600	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr4:87970200-87989800	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr4:87975000-87987800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr4:87976200-87989800	Weak transcription	Fetal Muscle Trunk	muscle
8	chr4:87977000-87989400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr4:87978200-87983600	Enhancers	Psoas Muscle	Psoas
10	chr4:87979000-87983400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr4:87979400-87983600	Strong transcription	Dnd41	blood
12	chr4:87979600-87990000	Weak transcription	Aorta	Aorta
13	chr4:87979800-87983200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr4:87979800-87984000	Strong transcription	Primary B cells from cord blood	blood
15	chr4:87979800-87989600	Weak transcription	Fetal Muscle Leg	muscle
16	chr4:87979800-87991800	Weak transcription	A549	lung
17	chr4:87980000-87990000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr4:87980000-87994000	Weak transcription	Primary monocytes fromperipheralblood	blood
19	chr4:87980200-87983600	Strong transcription	Fetal Thymus	thymus
20	chr4:87980200-87983600	Enhancers	Rectal Smooth Muscle	rectum
21	chr4:87980200-87989800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr4:87980400-87983600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
23	chr4:87980400-87988800	Weak transcription	Fetal Kidney	kidney
24	chr4:87980400-87989400	Weak transcription	Fetal Lung	lung
25	chr4:87980400-87989600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr4:87980600-87987400	Weak transcription	Lung	lung
27	chr4:87980600-87988400	Weak transcription	Brain Anterior Caudate	brain
28	chr4:87980600-87989800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
29	chr4:87980800-87984800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr4:87980800-87988000	Weak transcription	Fetal Heart	heart
31	chr4:87980800-87991000	Strong transcription	Monocytes-CD14+_RO01746	blood
32	chr4:87981000-87983800	Strong transcription	Primary hematopoietic stem cells	blood
33	chr4:87981000-87984200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr4:87981000-87988200	Weak transcription	Adipose Nuclei	Adipose
35	chr4:87981000-87988600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr4:87981000-87989800	Weak transcription	Brain Cingulate Gyrus	brain
37	chr4:87981000-87994600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr4:87981200-87983600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr4:87981200-87983600	Strong transcription	Placenta	Placenta
40	chr4:87981200-87987600	Weak transcription	Brain Substantia Nigra	brain
41	chr4:87981200-87988400	Weak transcription	Ovary	ovary
42	chr4:87981200-87988600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
43	chr4:87981200-87989600	Weak transcription	Brain Angular Gyrus	brain
44	chr4:87981200-87989600	Weak transcription	Spleen	Spleen
45	chr4:87981200-87990000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr4:87981200-87994000	Weak transcription	HUVEC	blood vessel
47	chr4:87981200-87994200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr4:87981400-87983600	Enhancers	HMEC	breast
49	chr4:87981600-87988200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr4:87981600-87988400	Weak transcription	Pancreatic Islets	Pancreatic Islet

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