Variant report

Variant	rs39615
Chromosome Location	chr5:154169590-154169591
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr5:154169453-154170269	Hela-S3	cervix:	n/a	n/a
2	CTCF	chr5:154169500-154169650	GM12869	blood:	n/a	n/a
3	CHD2	chr5:154169496-154169674	K562	blood:	n/a	n/a
4	POLR2A	chr5:154169375-154170222	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:154169242..154171344-chr5:154172525..154174056,2	MCF-7	breast:
2	chr5:154168441..154171085-chr5:154196369..154197910,2	MCF-7	breast:

Variant related genes	Relation type
LARP1	TF binding region
ENSG00000155506	Chromatin interaction

Extended variants
information (count: 158 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:157)

rs_ID	r²[population]
rs10042134	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13181649	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1390598	0.95[EUR][1000 genomes]
rs1390600	0.95[EUR][1000 genomes]
rs1390601	0.95[EUR][1000 genomes]
rs1390602	0.95[EUR][1000 genomes]
rs1390603	0.95[EUR][1000 genomes]
rs164192	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs164193	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs164194	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs164196	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs164198	1.00[CEU][hapmap];1.00[GIH][hapmap];0.90[EUR][1000 genomes]
rs164199	0.90[EUR][1000 genomes]
rs17116671	0.95[EUR][1000 genomes]
rs17116677	0.95[EUR][1000 genomes]
rs17116679	0.95[EUR][1000 genomes]
rs17116683	0.95[EUR][1000 genomes]
rs17116698	0.86[EUR][1000 genomes]
rs17116701	0.95[EUR][1000 genomes]
rs17570361	0.95[EUR][1000 genomes]
rs180903	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs184703	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs185323	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs186998	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs189439	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2059045	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2112219	0.90[EUR][1000 genomes]
rs2112220	1.00[CEU][hapmap]
rs2112222	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2544827	0.90[EUR][1000 genomes]
rs2544862	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2544870	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2544871	0.90[EUR][1000 genomes]
rs2544872	0.82[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2544873	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2544877	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2544881	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2544882	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2544883	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs2544885	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs255530	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs255531	0.80[ASN][1000 genomes]
rs2560069	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2644745	0.88[ASN][1000 genomes]
rs2644747	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs2644748	0.90[EUR][1000 genomes]
rs2688183	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2688185	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2688192	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2688202	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2688209	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs32426	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs346572	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs346573	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs348734	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs348736	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs348737	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs348738	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs348740	1.00[CEU][hapmap]
rs348746	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs348753	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs348755	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes]
rs348758	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3776982	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs39953	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs40584	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4958393	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4958769	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4958770	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4958772	0.86[EUR][1000 genomes]
rs4958774	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs58395756	0.95[EUR][1000 genomes]
rs59025588	0.90[EUR][1000 genomes]
rs59919514	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60476447	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs60906140	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61386671	0.86[EUR][1000 genomes]
rs61511229	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61554631	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6580117	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6580118	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6580119	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6580121	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6580124	0.95[EUR][1000 genomes]
rs6879093	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs702743	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73276745	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73276760	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73276766	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73276769	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73276780	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73278805	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73278819	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73278843	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73280717	0.90[EUR][1000 genomes]
rs73280724	0.90[EUR][1000 genomes]
rs73280726	0.90[EUR][1000 genomes]
rs73280747	0.90[EUR][1000 genomes]
rs73280749	0.90[EUR][1000 genomes]
rs73280750	0.90[EUR][1000 genomes]
rs73280761	1.00[EUR][1000 genomes]
rs73280762	1.00[EUR][1000 genomes]
rs73280768	1.00[EUR][1000 genomes]
rs73280770	0.95[EUR][1000 genomes]
rs73280778	0.95[EUR][1000 genomes]
rs73280785	0.95[EUR][1000 genomes]
rs73280786	0.95[EUR][1000 genomes]
rs73280788	0.95[EUR][1000 genomes]
rs73280792	0.95[EUR][1000 genomes]
rs73280795	0.95[EUR][1000 genomes]
rs73280797	0.90[EUR][1000 genomes]
rs73280799	0.95[EUR][1000 genomes]
rs73282508	0.95[EUR][1000 genomes]
rs73282513	0.95[EUR][1000 genomes]
rs73282516	0.95[EUR][1000 genomes]
rs73282519	0.95[EUR][1000 genomes]
rs73282521	0.95[EUR][1000 genomes]
rs73282522	0.86[EUR][1000 genomes]
rs73282523	0.95[EUR][1000 genomes]
rs73282525	0.95[EUR][1000 genomes]
rs73282527	0.95[EUR][1000 genomes]
rs73282528	0.95[EUR][1000 genomes]
rs73282530	0.86[EUR][1000 genomes]
rs73282533	0.95[EUR][1000 genomes]
rs73282538	0.95[EUR][1000 genomes]
rs73282539	0.95[EUR][1000 genomes]
rs73282553	0.95[EUR][1000 genomes]
rs73282555	0.95[EUR][1000 genomes]
rs73282558	0.95[EUR][1000 genomes]
rs7703040	0.95[EUR][1000 genomes]
rs7703227	0.95[EUR][1000 genomes]
rs7703386	0.95[EUR][1000 genomes]
rs7703765	0.95[EUR][1000 genomes]
rs7719208	0.95[EUR][1000 genomes]
rs7720521	0.82[ASN][1000 genomes]
rs7720538	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7722949	0.95[EUR][1000 genomes]
rs7723741	0.95[EUR][1000 genomes]
rs7724303	0.95[EUR][1000 genomes]
rs7724660	0.95[EUR][1000 genomes]
rs7727176	0.90[EUR][1000 genomes]
rs7733367	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs816715	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs816716	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs816724	0.85[EUR][1000 genomes]
rs816733	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs816736	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs816737	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs816738	0.90[EUR][1000 genomes]
rs816739	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs816740	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs816742	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs816744	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs816745	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs816746	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs816748	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs863650	1.00[CEU][hapmap];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830521	chr5:154147567-154244266	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:154151600-154171200	Weak transcription	Fetal Brain Male	brain
2	chr5:154161800-154169800	Weak transcription	HMEC	breast
3	chr5:154162400-154170200	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr5:154163000-154169600	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr5:154163000-154169800	Weak transcription	Fetal Brain Female	brain
6	chr5:154163000-154171200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr5:154163200-154169800	Weak transcription	NHLF	lung
8	chr5:154163400-154171200	Weak transcription	HSMMtube	muscle
9	chr5:154163600-154169800	Weak transcription	Primary B cells from cord blood	blood
10	chr5:154164000-154169800	Weak transcription	Brain Germinal Matrix	brain
11	chr5:154164000-154173600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr5:154164200-154176400	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr5:154164600-154188200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr5:154165000-154171000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr5:154165600-154169800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr5:154166000-154176000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr5:154166400-154169600	Weak transcription	HepG2	liver
18	chr5:154166400-154173200	Strong transcription	Fetal Intestine Small	intestine
19	chr5:154167000-154203000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr5:154167800-154169800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr5:154167800-154169800	Weak transcription	Liver	Liver
22	chr5:154167800-154171000	Weak transcription	HSMM	muscle
23	chr5:154167800-154171000	Weak transcription	NHDF-Ad	bronchial
24	chr5:154168000-154169600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr5:154168000-154169600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr5:154168000-154169600	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr5:154168000-154169600	Weak transcription	Esophagus	oesophagus
28	chr5:154168000-154169600	Weak transcription	Rectal Mucosa Donor 29	rectum
29	chr5:154168000-154169600	Weak transcription	Osteobl	bone
30	chr5:154168000-154169800	Weak transcription	Brain Hippocampus Middle	brain
31	chr5:154168000-154169800	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr5:154168000-154171000	Weak transcription	Brain Cingulate Gyrus	brain
33	chr5:154168000-154171200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr5:154168000-154171400	Weak transcription	Fetal Kidney	kidney
35	chr5:154168000-154171600	Weak transcription	Stomach Mucosa	stomach
36	chr5:154168000-154174600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
37	chr5:154168200-154169600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr5:154168200-154169600	Weak transcription	Primary B cells from peripheral blood	blood
39	chr5:154168200-154169600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
40	chr5:154168200-154169600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
41	chr5:154168200-154169600	Weak transcription	Muscle Satellite Cultured Cells	--
42	chr5:154168200-154169600	Weak transcription	Adipose Nuclei	Adipose
43	chr5:154168200-154169600	Weak transcription	Aorta	Aorta
44	chr5:154168200-154169600	Weak transcription	Brain Angular Gyrus	brain
45	chr5:154168200-154169600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr5:154168200-154169600	Weak transcription	Fetal Muscle Leg	muscle
47	chr5:154168200-154169600	Weak transcription	Placenta	Placenta
48	chr5:154168200-154169600	Weak transcription	Left Ventricle	heart
49	chr5:154168200-154169600	Weak transcription	Lung	lung
50	chr5:154168200-154169600	Weak transcription	Ovary	ovary

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