Variant report

Variant	rs16872556
Chromosome Location	chr5:74710550-74710551
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 67 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs1018119	1.00[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs10515195	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10942736	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10942737	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12055331	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16872521	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16872526	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs16872528	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16872536	0.86[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];0.82[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16872555	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16872589	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs16872635	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs1909720	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs1988728	1.00[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs2303152	1.00[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];0.91[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.91[MKK][hapmap];0.83[AFR][1000 genomes];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3827608	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3857388	0.85[CEU][hapmap];0.88[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap]
rs3895886	0.85[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap]
rs3925086	0.82[AFR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4629571	0.83[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs55805408	0.82[AFR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56082155	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56361267	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56981407	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs5744566	1.00[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.80[ASN][1000 genomes]
rs5744567	1.00[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.80[ASN][1000 genomes]
rs5744572	0.80[ASN][1000 genomes]
rs5744578	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs5744591	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs5744594	0.86[AFR][1000 genomes]
rs5744612	1.00[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];0.91[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs5744661	0.86[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs57566899	0.80[AFR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs58780510	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59367133	0.82[AFR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs60298841	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs60854109	0.86[AFR][1000 genomes]
rs61001560	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61080643	0.82[AFR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61175242	0.86[AFR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61678717	0.82[AFR][1000 genomes]
rs6878576	0.85[CEU][hapmap];0.88[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap]
rs73763057	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73763093	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73763094	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73763097	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73763098	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73763099	0.86[AFR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73763101	0.86[AFR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73763102	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73764903	0.82[AFR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73764904	0.86[AFR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73764905	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73764909	0.86[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs73764910	0.86[AFR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73764914	0.86[AFR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73764915	0.80[ASN][1000 genomes]
rs73764920	0.86[AFR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73764921	0.82[AFR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73764922	0.82[AFR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73764925	0.86[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs9791146	0.89[EUR][1000 genomes];0.89[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	nsv882193	chr5:74656175-74917862	ZNF genes & repeats Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv882194	chr5:74656175-74946455	Strong transcription Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv882195	chr5:74678937-74896798	Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
4	nsv882196	chr5:74678937-74917862	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
5	nsv882197	chr5:74692776-74946455	Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:74656400-74725600	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr5:74656800-74731400	Weak transcription	Rectal Smooth Muscle	rectum
3	chr5:74659800-74720600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr5:74660000-74722800	Weak transcription	Fetal Heart	heart
5	chr5:74667000-74723200	Strong transcription	Monocytes-CD14+_RO01746	blood
6	chr5:74670800-74720600	Weak transcription	Right Ventricle	heart
7	chr5:74670800-74731400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr5:74671000-74722800	Weak transcription	Hela-S3	cervix
9	chr5:74674400-74761400	Weak transcription	Esophagus	oesophagus
10	chr5:74675400-74720800	Weak transcription	Small Intestine	intestine
11	chr5:74676200-74721000	Weak transcription	Brain Hippocampus Middle	brain
12	chr5:74677400-74722800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr5:74677600-74734200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr5:74677800-74721000	Weak transcription	NH-A	brain
15	chr5:74677800-74725000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
16	chr5:74677800-74731400	Weak transcription	Aorta	Aorta
17	chr5:74678000-74720600	Weak transcription	Colonic Mucosa	Colon
18	chr5:74678000-74730800	Weak transcription	Psoas Muscle	Psoas
19	chr5:74680600-74721000	Weak transcription	HMEC	breast
20	chr5:74680800-74722600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
21	chr5:74681000-74723200	Weak transcription	HUVEC	blood vessel
22	chr5:74681400-74718400	Weak transcription	Brain Germinal Matrix	brain
23	chr5:74681800-74720600	Weak transcription	Fetal Brain Male	brain
24	chr5:74684000-74720400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
25	chr5:74684000-74720800	Weak transcription	Thymus	Thymus
26	chr5:74684000-74731200	Weak transcription	HSMMtube	muscle
27	chr5:74685800-74711800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr5:74695200-74718200	Weak transcription	Colon Smooth Muscle	Colon
29	chr5:74695400-74721000	Weak transcription	Brain Anterior Caudate	brain
30	chr5:74695400-74721000	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr5:74695400-74723200	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr5:74695600-74721000	Weak transcription	Brain Angular Gyrus	brain
33	chr5:74696000-74715800	Weak transcription	Ovary	ovary
34	chr5:74696200-74713800	Weak transcription	Fetal Brain Female	brain
35	chr5:74697000-74714000	Weak transcription	Skeletal Muscle Female	skeletal muscle
36	chr5:74697000-74720400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
37	chr5:74697200-74714000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
38	chr5:74697400-74714200	Weak transcription	Stomach Smooth Muscle	stomach
39	chr5:74698000-74711200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
40	chr5:74698000-74712200	Weak transcription	Duodenum Mucosa	Duodenum
41	chr5:74698000-74714000	Weak transcription	Fetal Kidney	kidney
42	chr5:74699400-74715800	Weak transcription	Primary hematopoietic stem cells	blood
43	chr5:74699600-74710600	Weak transcription	HSMM	muscle
44	chr5:74699600-74731200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
45	chr5:74700000-74711200	Weak transcription	Placenta	Placenta
46	chr5:74700400-74710800	Weak transcription	Rectal Mucosa Donor 29	rectum
47	chr5:74702000-74721000	Weak transcription	A549	lung
48	chr5:74703800-74722600	Strong transcription	Primary monocytes fromperipheralblood	blood
49	chr5:74703800-74723000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
50	chr5:74704200-74722000	Strong transcription	Primary B cells from peripheral blood	blood

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