Variant report

Variant	rs317872
Chromosome Location	chr4:16186347-16186348
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:16184108..16186493-chr4:16187393..16189533,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000169762	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10006159	0.82[YRI][hapmap]
rs10019399	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1025897	0.80[YRI][hapmap]
rs1046234	0.85[YRI][hapmap]
rs10516299	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs10939651	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10939652	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10939653	0.81[ASN][1000 genomes]
rs12506249	0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12646600	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13133263	0.95[YRI][hapmap];0.81[AFR][1000 genomes]
rs13634	0.95[YRI][hapmap]
rs1373112	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs1619904	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1662650	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1662654	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1662656	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16893162	0.95[YRI][hapmap]
rs1712492	0.95[YRI][hapmap]
rs178450	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs203434	0.90[YRI][hapmap]
rs2044195	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28453363	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28618674	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28645901	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs317854	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs317855	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs317869	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs317870	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs317871	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs317873	0.95[YRI][hapmap];0.81[AFR][1000 genomes]
rs317874	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs317875	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs317876	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs317877	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs317878	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs36012247	0.81[AFR][1000 genomes]
rs4395495	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6812660	0.95[YRI][hapmap]
rs7657191	0.84[ASN][1000 genomes]
rs7666361	0.81[AFR][1000 genomes]
rs961449	0.90[YRI][hapmap]

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	nsv998299	chr4:16031459-16226466	Bivalent/Poised TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
2	nsv1004821	chr4:16055996-16830629	Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv537046	chr4:16055996-16830629	Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Weak transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
4	nsv537047	chr4:16182060-16375787	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:16161800-16193200	Strong transcription	Monocytes-CD14+_RO01746	blood
2	chr4:16163200-16195800	Weak transcription	HMEC	breast
3	chr4:16164400-16195000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr4:16165000-16190800	Weak transcription	HUVEC	blood vessel
5	chr4:16168000-16208000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr4:16168000-16213800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr4:16168200-16187400	Weak transcription	Osteobl	bone
8	chr4:16168200-16198000	Weak transcription	A549	lung
9	chr4:16168400-16194600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr4:16168400-16197800	Weak transcription	NHLF	lung
11	chr4:16168400-16198000	Weak transcription	NH-A	brain
12	chr4:16168600-16191000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr4:16168600-16198000	Weak transcription	NHEK	skin
14	chr4:16170400-16191400	Weak transcription	Colonic Mucosa	Colon
15	chr4:16170600-16191000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr4:16170800-16208000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr4:16171400-16207200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr4:16171600-16191000	Weak transcription	Esophagus	oesophagus
19	chr4:16171600-16191600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr4:16171600-16194400	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr4:16171600-16198000	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr4:16172000-16187200	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr4:16172000-16191000	Weak transcription	Pancreas	Pancrea
24	chr4:16172000-16191000	Weak transcription	Small Intestine	intestine
25	chr4:16172000-16191000	Weak transcription	Spleen	Spleen
26	chr4:16172000-16198000	Weak transcription	HSMMtube	muscle
27	chr4:16172200-16190800	Weak transcription	Right Ventricle	heart
28	chr4:16172400-16187400	Weak transcription	Fetal Kidney	kidney
29	chr4:16172600-16191000	Weak transcription	Fetal Brain Female	brain
30	chr4:16172800-16190800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr4:16174400-16196800	Weak transcription	Stomach Mucosa	stomach
32	chr4:16175000-16187200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr4:16175000-16187400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
34	chr4:16176000-16191200	Weak transcription	NHDF-Ad	bronchial
35	chr4:16176200-16198000	Weak transcription	HSMM	muscle
36	chr4:16177000-16194000	Weak transcription	Pancreatic Islets	Pancreatic Islet
37	chr4:16178600-16188000	Weak transcription	Cortex derived primary cultured neurospheres	brain
38	chr4:16178800-16187200	Weak transcription	Lung	lung
39	chr4:16178800-16191000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr4:16178800-16191400	Weak transcription	Gastric	stomach
41	chr4:16179200-16196000	Weak transcription	Fetal Heart	heart
42	chr4:16179800-16187000	Weak transcription	Fetal Stomach	stomach
43	chr4:16179800-16187200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
44	chr4:16180400-16187800	Weak transcription	HUES64 Cell Line	embryonic stem cell
45	chr4:16180600-16187400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
46	chr4:16180800-16192600	Weak transcription	H9 Cell Line	embryonic stem cell
47	chr4:16181000-16186800	Weak transcription	Fetal Muscle Trunk	muscle
48	chr4:16181000-16187200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr4:16181000-16187200	Weak transcription	Ovary	ovary
50	chr4:16181000-16190600	Weak transcription	K562	blood

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