Variant report

Variant	rs17668952
Chromosome Location	chr4:88003262-88003263
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:87929301..87933851-chr4:88000404..88005339,4	K562	blood:
2	chr4:87997558..88001299-chr4:88002036..88005142,4	K562	blood:
3	chr4:87926997..87929078-chr4:88000294..88003614,4	K562	blood:
4	chr4:88002713..88005662-chr4:88048003..88049629,2	K562	blood:
5	chr4:88003148..88004753-chr4:88140002..88142536,2	MCF-7	breast:
6	chr4:87926997..87929975-chr4:88000498..88004570,5	K562	blood:
7	chr4:87855032..87857925-chr4:88002674..88004919,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000145332	Chromatin interaction
ENSG00000172493	Chromatin interaction
ENSG00000163633	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10003331	1.00[ASN][1000 genomes]
rs10015544	1.00[ASN][1000 genomes]
rs10022825	1.00[ASN][1000 genomes]
rs10032200	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs10050309	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1037813	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10489044	1.00[ASW][hapmap]
rs12508231	1.00[ASN][1000 genomes]
rs12646299	1.00[YRI][hapmap]
rs13103234	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13108043	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13134084	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17012304	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs17030453	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17604937	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17668731	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.95[MKK][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]
rs17703261	1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2230858	1.00[ASN][1000 genomes]
rs28495374	1.00[ASN][1000 genomes]
rs28667805	1.00[ASN][1000 genomes]
rs28791499	1.00[ASN][1000 genomes]
rs35658582	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35849753	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs366327	0.86[CEU][hapmap];1.00[CHB][hapmap];0.96[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs431836	1.00[ASW][hapmap]
rs4693158	1.00[YRI][hapmap]
rs56656813	1.00[ASN][1000 genomes]
rs57954253	1.00[ASN][1000 genomes]
rs58478399	1.00[ASN][1000 genomes]
rs59526367	1.00[ASN][1000 genomes]
rs62306540	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6817981	1.00[ASN][1000 genomes]
rs6822384	1.00[ASN][1000 genomes]
rs6846149	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6846352	1.00[ASN][1000 genomes]
rs71607404	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72877916	1.00[ASN][1000 genomes]
rs72877918	1.00[ASN][1000 genomes]
rs73839171	1.00[ASN][1000 genomes]
rs7664479	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7668285	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs967552	1.00[YRI][hapmap]

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:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:87990200-88008000	Weak transcription	Spleen	Spleen
2	chr4:87995200-88009400	Weak transcription	HepG2	liver
3	chr4:87995200-88010600	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr4:87995200-88029200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr4:87995400-88006200	Weak transcription	Hela-S3	cervix
6	chr4:87995400-88037800	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr4:87995600-88005200	Weak transcription	Primary monocytes fromperipheralblood	blood
8	chr4:87995600-88011200	Weak transcription	Colonic Mucosa	Colon
9	chr4:87995800-88005200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr4:87995800-88005200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr4:87995800-88023800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr4:87996000-88005400	Weak transcription	Primary T cells from cord blood	blood
13	chr4:87996000-88005400	Weak transcription	Monocytes-CD14+_RO01746	blood
14	chr4:87996000-88005800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr4:87996200-88005200	Weak transcription	Primary T helper cells fromperipheralblood	blood
16	chr4:87996400-88005000	Weak transcription	Primary B cells from cord blood	blood
17	chr4:87996800-88004400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr4:87996800-88023600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
19	chr4:87997800-88004400	Enhancers	Duodenum Smooth Muscle	Duodenum
20	chr4:87998600-88003600	Enhancers	NHDF-Ad	bronchial
21	chr4:87998800-88008000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr4:87999000-88005400	Enhancers	Adipose Nuclei	Adipose
23	chr4:87999400-88006000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr4:87999400-88007600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr4:87999400-88010600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr4:87999600-88006400	Enhancers	Rectal Smooth Muscle	rectum
27	chr4:87999600-88008200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr4:87999600-88010600	Weak transcription	Primary T helper cells PMA-I stimulated	--
29	chr4:87999600-88011000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr4:87999800-88003600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
31	chr4:87999800-88004200	Enhancers	Brain Substantia Nigra	brain
32	chr4:87999800-88004400	Enhancers	Brain Angular Gyrus	brain
33	chr4:87999800-88004600	Enhancers	Brain Anterior Caudate	brain
34	chr4:87999800-88005000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr4:87999800-88005200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr4:87999800-88007000	Weak transcription	Duodenum Mucosa	Duodenum
37	chr4:88000000-88007000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr4:88000200-88005400	Enhancers	Colon Smooth Muscle	Colon
39	chr4:88000200-88010600	Weak transcription	HUES64 Cell Line	embryonic stem cell
40	chr4:88000400-88005200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
41	chr4:88000400-88007400	Weak transcription	HUES48 Cell Line	embryonic stem cell
42	chr4:88000400-88020800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr4:88000600-88003400	Enhancers	Brain Inferior Temporal Lobe	brain
44	chr4:88000600-88006600	Enhancers	Skeletal Muscle Male	skeletal muscle
45	chr4:88000600-88008400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr4:88000600-88013000	Weak transcription	A549	lung
47	chr4:88000800-88003800	Weak transcription	Fetal Brain Female	brain
48	chr4:88000800-88004200	Enhancers	Brain Cingulate Gyrus	brain
49	chr4:88000800-88004800	Weak transcription	HUES6 Cell Line	embryonic stem cell
50	chr4:88000800-88005200	Weak transcription	Primary neutrophils fromperipheralblood	blood

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