Variant report

Variant	rs4924673
Chromosome Location	chr15:42621801-42621802
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 96 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:91)

rs_ID	r²[population]
rs10220859	0.85[CHB][hapmap]
rs12437600	0.87[ASN][1000 genomes]
rs12438240	0.86[CHB][hapmap]
rs12438369	0.85[CHB][hapmap];0.91[YRI][hapmap];0.89[ASN][1000 genomes]
rs12438453	0.86[CHB][hapmap];0.88[YRI][hapmap]
rs12438509	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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[JPT][hapmap];0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12441016	0.89[ASN][1000 genomes]
rs12441642	0.86[CHB][hapmap];1.00[JPT][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];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1659221	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1659222	1.00[CEU][hapmap];0.87[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]
rs16972770	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs16972776	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes]
rs16972779	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16972887	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.88[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs16973008	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[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];0.93[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];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1703754	1.00[CEU][hapmap]
rs2138831	0.85[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2407707	0.86[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.80[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs2412688	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2412709	0.85[CHB][hapmap]
rs2620386	1.00[CEU][hapmap]
rs28364388	0.89[ASN][1000 genomes]
rs28364390	0.84[ASN][1000 genomes]
rs28364393	1.00[CHB][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]
rs3736099	0.83[ASN][1000 genomes]
rs3742996	0.85[CHB][hapmap]
rs3743005	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]
rs3743007	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]
rs3743008	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]
rs3825785	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]
rs4506867	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[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[JPT][hapmap];0.83[ASN][1000 genomes]
rs4923945	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]
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[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]
rs4924674	0.85[CHB][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	0.89[ASN][1000 genomes]
rs56987883	0.94[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	1.00[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	0.94[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	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59094161	0.94[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	0.98[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	0.81[AFR][1000 genomes];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	0.94[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]
rs681029	1.00[CEU][hapmap]
rs7179203	0.89[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[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]
rs7181979	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs73398938	0.87[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	0.93[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]
rs8025601	0.86[CHB][hapmap];0.89[ASN][1000 genomes]
rs8027016	0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs8041951	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:42567200-42623600	Weak transcription	Fetal Brain Male	brain
2	chr15:42568400-42656000	Weak transcription	Small Intestine	intestine
3	chr15:42568600-42630800	Weak transcription	Dnd41	blood
4	chr15:42573400-42635800	Weak transcription	Gastric	stomach
5	chr15:42585400-42623600	Weak transcription	Colon Smooth Muscle	Colon
6	chr15:42596800-42625200	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr15:42600400-42626400	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr15:42600600-42627200	Weak transcription	Fetal Brain Female	brain
9	chr15:42601200-42636000	Weak transcription	Brain Germinal Matrix	brain
10	chr15:42603200-42627200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr15:42603200-42636000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr15:42603400-42622400	Weak transcription	Fetal Heart	heart
13	chr15:42603400-42623200	Weak transcription	Brain Angular Gyrus	brain
14	chr15:42603400-42648600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr15:42603400-42648600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr15:42604000-42639400	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr15:42604600-42651200	Weak transcription	Fetal Kidney	kidney
18	chr15:42606200-42634600	Weak transcription	Pancreas	Pancrea
19	chr15:42613000-42622200	Strong transcription	Duodenum Mucosa	Duodenum
20	chr15:42613000-42623800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr15:42613000-42624000	Strong transcription	Primary monocytes fromperipheralblood	blood
22	chr15:42613000-42624000	Strong transcription	Monocytes-CD14+_RO01746	blood
23	chr15:42613400-42624200	Strong transcription	Primary B cells from cord blood	blood
24	chr15:42613400-42626400	Strong transcription	Primary B cells from peripheral blood	blood
25	chr15:42613600-42622200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr15:42613600-42623800	Strong transcription	Adipose Nuclei	Adipose
27	chr15:42613800-42623800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr15:42614000-42623800	Strong transcription	Liver	Liver
29	chr15:42614200-42623800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr15:42614200-42624600	Weak transcription	HUVEC	blood vessel
31	chr15:42614200-42624800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
32	chr15:42614800-42627200	Weak transcription	Psoas Muscle	Psoas
33	chr15:42615000-42627200	Weak transcription	Fetal Intestine Small	intestine
34	chr15:42615600-42623000	Weak transcription	Esophagus	oesophagus
35	chr15:42615600-42625600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr15:42615600-42629000	Weak transcription	Right Ventricle	heart
37	chr15:42615600-42631800	Weak transcription	Lung	lung
38	chr15:42616200-42622000	Weak transcription	Fetal Muscle Trunk	muscle
39	chr15:42616200-42634600	Weak transcription	Fetal Stomach	stomach
40	chr15:42616200-42636600	Weak transcription	NHEK	skin
41	chr15:42616600-42623400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr15:42616800-42623400	Weak transcription	HSMMtube	muscle
43	chr15:42616800-42624400	Weak transcription	Muscle Satellite Cultured Cells	--
44	chr15:42616800-42636000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr15:42617000-42622400	Weak transcription	Hela-S3	cervix
46	chr15:42617000-42645000	Weak transcription	NHLF	lung
47	chr15:42617600-42622400	Strong transcription	Rectal Mucosa Donor 29	rectum
48	chr15:42617800-42623600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr15:42618000-42636000	Weak transcription	Colonic Mucosa	Colon
50	chr15:42618200-42623600	Strong transcription	Breast Myoepithelial Primary Cells	Breast

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