Variant report

Variant	rs3743005
Chromosome Location	chr15:42645892-42645893
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 105 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:98)

rs_ID	r²[population]
rs11070370	0.80[MEX][hapmap]
rs12437600	0.87[ASN][1000 genomes]
rs12438240	0.85[CHB][hapmap]
rs12438369	1.00[ASW][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[LWK][hapmap];0.85[MEX][hapmap];0.94[MKK][hapmap];0.91[YRI][hapmap];0.86[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs12438453	0.85[CHB][hapmap];0.91[YRI][hapmap];0.85[AFR][1000 genomes]
rs12438509	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.94[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12440087	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12441016	0.89[ASN][1000 genomes]
rs12441642	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs12441700	0.80[MEX][hapmap]
rs1359003	0.80[MEX][hapmap]
rs1624183	1.00[CEU][hapmap]
rs1659213	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1659218	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1659219	1.00[CEU][hapmap];0.94[MEX][hapmap];0.91[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1659221	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1659222	1.00[CEU][hapmap];0.94[MEX][hapmap];0.91[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1678984	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1678992	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1678993	0.81[AMR][1000 genomes]
rs16972776	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.86[GIH][hapmap];0.94[MEX][hapmap];0.90[TSI][hapmap];0.82[AMR][1000 genomes]
rs16972779	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs16972887	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.88[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs16973008	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16973045	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16973060	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2138831	0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.81[ASN][1000 genomes]
rs2407707	0.85[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.88[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs2412688	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2412709	0.81[ASW][hapmap];0.85[CHB][hapmap]
rs28364388	0.82[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs28364390	0.85[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs28364393	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2918460	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2918461	0.80[MEX][hapmap]
rs3736099	0.83[ASN][1000 genomes]
rs3742996	0.81[ASW][hapmap];0.85[CHB][hapmap]
rs3743006	0.85[MEX][hapmap]
rs3743007	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs3743008	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs3825785	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][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]
rs4506867	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4923932	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.88[TSI][hapmap];0.83[ASN][1000 genomes]
rs4923945	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4924627	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4924630	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4924631	0.81[ASN][1000 genomes]
rs4924644	0.90[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4924672	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4924673	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4924674	0.85[CHB][hapmap];1.00[CHD][hapmap];0.80[MEX][hapmap];0.89[ASN][1000 genomes]
rs55882551	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56257215	0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs56670003	0.94[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs56702977	0.84[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs56987883	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57134130	0.89[ASN][1000 genomes]
rs57393446	0.91[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs57933952	0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs57973092	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57976413	0.94[ASN][1000 genomes]
rs58292736	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs58313689	0.86[ASN][1000 genomes]
rs58712370	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59094161	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59132828	0.89[ASN][1000 genomes]
rs59138723	0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs59320762	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59893734	0.83[ASN][1000 genomes]
rs59974698	0.95[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs60443443	0.83[ASN][1000 genomes]
rs60634548	0.94[ASN][1000 genomes]
rs61069354	0.94[ASN][1000 genomes]
rs61133768	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6493033	0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs678778	1.00[CEU][hapmap]
rs7179203	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7179709	1.00[CEU][hapmap]
rs7180279	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][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]
rs7181979	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7183546	0.85[MEX][hapmap]
rs73398938	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73400993	0.95[ASN][1000 genomes]
rs73402707	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73403365	0.94[ASN][1000 genomes]
rs73407403	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73407407	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs73407488	0.94[ASN][1000 genomes]
rs73409577	0.92[ASN][1000 genomes]
rs751572	0.80[MEX][hapmap]
rs8024732	0.80[MEX][hapmap]
rs8025601	0.85[CHB][hapmap];0.89[ASN][1000 genomes]
rs8027016	0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs8031315	0.80[MEX][hapmap]
rs8036596	0.80[MEX][hapmap]
rs8037020	0.84[MEX][hapmap]
rs8041951	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9920921	0.85[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931223	chr15:41989960-42781757	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
2	nsv1049445	chr15:42239738-42830484	Enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
3	nsv542366	chr15:42239738-42830484	Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
4	nsv904133	chr15:42528982-42681057	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
5	nsv832986	chr15:42587825-42753664	Genic enhancers Weak transcription Strong transcription Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv832987	chr15:42627447-42792348	Active TSS Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
7	nsv932995	chr15:42640015-42704121	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:42568400-42656000	Weak transcription	Small Intestine	intestine
2	chr15:42603400-42648600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr15:42603400-42648600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr15:42604600-42651200	Weak transcription	Fetal Kidney	kidney
5	chr15:42619600-42647200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
6	chr15:42619600-42656200	Weak transcription	HMEC	breast
7	chr15:42627600-42654600	Weak transcription	HSMM	muscle
8	chr15:42630600-42650600	Strong transcription	Monocytes-CD14+_RO01746	blood
9	chr15:42630800-42646800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
10	chr15:42631600-42648600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr15:42631600-42649800	Strong transcription	Primary monocytes fromperipheralblood	blood
12	chr15:42631800-42649400	Weak transcription	Fetal Brain Male	brain
13	chr15:42631800-42651000	Weak transcription	Fetal Heart	heart
14	chr15:42632200-42652600	Strong transcription	Primary B cells from peripheral blood	blood
15	chr15:42634600-42648000	Strong transcription	Sigmoid Colon	Sigmoid Colon
16	chr15:42634600-42648200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr15:42634600-42650400	Strong transcription	Rectal Mucosa Donor 29	rectum
18	chr15:42635200-42646400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr15:42636400-42646400	Weak transcription	Fetal Brain Female	brain
20	chr15:42636400-42647800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr15:42636400-42656600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr15:42637200-42653600	Weak transcription	Brain Germinal Matrix	brain
23	chr15:42637600-42647000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr15:42638400-42651800	Weak transcription	Psoas Muscle	Psoas
25	chr15:42638600-42646000	Strong transcription	Skeletal Muscle Female	skeletal muscle
26	chr15:42639000-42646400	Strong transcription	Fetal Muscle Leg	muscle
27	chr15:42639400-42658600	Weak transcription	Hela-S3	cervix
28	chr15:42639800-42652200	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr15:42640200-42649800	Strong transcription	Primary T cells fromperipheralblood	blood
30	chr15:42641400-42657400	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr15:42641800-42648600	Weak transcription	NH-A	brain
32	chr15:42641800-42649600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr15:42641800-42652800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr15:42642400-42655400	Weak transcription	Muscle Satellite Cultured Cells	--
35	chr15:42642600-42648200	Strong transcription	Primary T helper cells fromperipheralblood	blood
36	chr15:42643000-42650400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr15:42643000-42650800	Strong transcription	Adipose Nuclei	Adipose
38	chr15:42643000-42654800	Strong transcription	Liver	Liver
39	chr15:42643200-42646200	Strong transcription	Brain Anterior Caudate	brain
40	chr15:42643200-42647400	Strong transcription	Primary hematopoietic stem cells	blood
41	chr15:42643200-42647400	Strong transcription	Rectal Mucosa Donor 31	rectum
42	chr15:42643200-42647600	Strong transcription	Duodenum Mucosa	Duodenum
43	chr15:42643200-42647800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr15:42643200-42647800	Strong transcription	Lung	lung
45	chr15:42643200-42650800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr15:42643400-42646000	Strong transcription	Brain Hippocampus Middle	brain
47	chr15:42643400-42646000	Strong transcription	Brain Substantia Nigra	brain
48	chr15:42643400-42646000	Strong transcription	Duodenum Smooth Muscle	Duodenum
49	chr15:42643400-42646200	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
50	chr15:42643400-42646200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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