Variant report

Variant	rs317873
Chromosome Location	chr4:16184441-16184442
allele	G/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: 1 )

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

rs_ID	r²[population]
rs10006159	0.91[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.85[YRI][hapmap];0.84[AFR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10019399	0.95[YRI][hapmap];0.81[AFR][1000 genomes]
rs1025897	0.87[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.94[JPT][hapmap];0.97[LWK][hapmap];0.94[MKK][hapmap];0.82[TSI][hapmap];0.85[YRI][hapmap];0.89[AFR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1046234	1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs10939652	0.81[AFR][1000 genomes]
rs10939657	0.83[ASN][1000 genomes]
rs11730977	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13133263	0.91[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13151111	0.81[ASN][1000 genomes]
rs13634	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1618243	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1662654	0.95[YRI][hapmap]
rs16893162	0.81[ASW][hapmap];0.97[LWK][hapmap];0.84[MKK][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs1712492	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1712495	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs178450	0.95[YRI][hapmap];0.82[AFR][1000 genomes]
rs203434	0.82[ASW][hapmap];0.82[CEU][hapmap];0.92[CHD][hapmap];0.86[GIH][hapmap];0.88[JPT][hapmap];0.89[LWK][hapmap];0.90[MKK][hapmap];0.95[YRI][hapmap];0.86[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs203435	0.88[JPT][hapmap]
rs28618674	0.81[AFR][1000 genomes]
rs317853	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs317854	0.95[YRI][hapmap]
rs317856	0.83[ASN][1000 genomes]
rs317857	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs317862	0.82[AMR][1000 genomes]
rs317866	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs317869	0.95[YRI][hapmap];0.81[AFR][1000 genomes]
rs317870	0.95[YRI][hapmap];0.81[AFR][1000 genomes]
rs317871	0.81[AFR][1000 genomes]
rs317872	0.95[YRI][hapmap];0.81[AFR][1000 genomes]
rs317875	0.95[YRI][hapmap];0.81[AFR][1000 genomes]
rs317876	0.95[YRI][hapmap];0.80[AFR][1000 genomes]
rs317877	0.94[YRI][hapmap]
rs317878	0.90[YRI][hapmap]
rs317909	0.80[AMR][1000 genomes]
rs36012247	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4317201	0.86[ASN][1000 genomes]
rs57924303	0.85[AFR][1000 genomes]
rs6812660	0.87[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];0.95[MKK][hapmap];0.82[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73130438	0.85[AFR][1000 genomes]
rs73130457	0.81[AFR][1000 genomes]
rs7666361	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs961449	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];0.92[MKK][hapmap];0.82[TSI][hapmap];0.95[YRI][hapmap];0.92[AFR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]

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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs317873	FAHD2B	trans	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:16161600-16186000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr4:16161800-16193200	Strong transcription	Monocytes-CD14+_RO01746	blood
3	chr4:16163200-16195800	Weak transcription	HMEC	breast
4	chr4:16164400-16195000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr4:16165000-16190800	Weak transcription	HUVEC	blood vessel
6	chr4:16168000-16208000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr4:16168000-16213800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr4:16168200-16187400	Weak transcription	Osteobl	bone
9	chr4:16168200-16198000	Weak transcription	A549	lung
10	chr4:16168400-16194600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr4:16168400-16197800	Weak transcription	NHLF	lung
12	chr4:16168400-16198000	Weak transcription	NH-A	brain
13	chr4:16168600-16191000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr4:16168600-16198000	Weak transcription	NHEK	skin
15	chr4:16170400-16191400	Weak transcription	Colonic Mucosa	Colon
16	chr4:16170600-16191000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr4:16170800-16208000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr4:16171400-16207200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr4:16171600-16191000	Weak transcription	Esophagus	oesophagus
20	chr4:16171600-16191600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr4:16171600-16194400	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr4:16171600-16198000	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr4:16172000-16187200	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr4:16172000-16191000	Weak transcription	Pancreas	Pancrea
25	chr4:16172000-16191000	Weak transcription	Small Intestine	intestine
26	chr4:16172000-16191000	Weak transcription	Spleen	Spleen
27	chr4:16172000-16198000	Weak transcription	HSMMtube	muscle
28	chr4:16172200-16190800	Weak transcription	Right Ventricle	heart
29	chr4:16172400-16187400	Weak transcription	Fetal Kidney	kidney
30	chr4:16172600-16191000	Weak transcription	Fetal Brain Female	brain
31	chr4:16172800-16190800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr4:16174400-16196800	Weak transcription	Stomach Mucosa	stomach
33	chr4:16175000-16187200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr4:16175000-16187400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
35	chr4:16176000-16191200	Weak transcription	NHDF-Ad	bronchial
36	chr4:16176200-16198000	Weak transcription	HSMM	muscle
37	chr4:16177000-16194000	Weak transcription	Pancreatic Islets	Pancreatic Islet
38	chr4:16178600-16188000	Weak transcription	Cortex derived primary cultured neurospheres	brain
39	chr4:16178800-16187200	Weak transcription	Lung	lung
40	chr4:16178800-16191000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr4:16178800-16191400	Weak transcription	Gastric	stomach
42	chr4:16179200-16196000	Weak transcription	Fetal Heart	heart
43	chr4:16179800-16187000	Weak transcription	Fetal Stomach	stomach
44	chr4:16179800-16187200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
45	chr4:16180400-16187800	Weak transcription	HUES64 Cell Line	embryonic stem cell
46	chr4:16180600-16185400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
47	chr4:16180600-16187400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
48	chr4:16180800-16192600	Weak transcription	H9 Cell Line	embryonic stem cell
49	chr4:16181000-16186000	Weak transcription	Primary T cells fromperipheralblood	blood
50	chr4:16181000-16186800	Weak transcription	Fetal Muscle Trunk	muscle

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