Variant report

Variant	rs12109050
Chromosome Location	chr5:16534093-16534094
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:16529119..16532127-chr5:16532204..16536269,4	MCF-7	breast:
2	chr5:16527152..16530063-chr5:16533839..16538809,7	K562	blood:

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10053236	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1020952	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1240951	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs1240952	0.91[CEU][hapmap];0.81[EUR][1000 genomes]
rs1551936	0.92[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs162758	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]
rs162862	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1991468	0.93[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs1991469	0.93[CHB][hapmap];0.87[JPT][hapmap];0.94[ASN][1000 genomes]
rs1991470	0.93[ASN][1000 genomes]
rs1991471	0.85[CHB][hapmap];0.87[JPT][hapmap];0.93[ASN][1000 genomes]
rs1991472	0.85[CHB][hapmap];0.87[JPT][hapmap];0.93[ASN][1000 genomes]
rs2019248	0.94[ASN][1000 genomes]
rs2019260	0.92[CHB][hapmap];0.87[JPT][hapmap];0.94[ASN][1000 genomes]
rs248132	0.90[CEU][hapmap]
rs248133	0.80[EUR][1000 genomes]
rs2560830	0.93[CHB][hapmap];0.92[JPT][hapmap];0.94[ASN][1000 genomes]
rs2560831	0.86[ASN][1000 genomes]
rs2617422	0.93[CHB][hapmap];0.86[JPT][hapmap];0.94[ASN][1000 genomes]
rs2617423	0.91[CHB][hapmap];0.94[ASN][1000 genomes]
rs2617424	0.93[CHB][hapmap];0.87[JPT][hapmap];0.94[ASN][1000 genomes]
rs2617425	0.92[CHB][hapmap];0.85[JPT][hapmap];0.94[ASN][1000 genomes]
rs2617426	0.92[CHB][hapmap];0.92[ASN][1000 genomes]
rs31283	0.92[CHB][hapmap];0.90[ASN][1000 genomes]
rs31288	0.86[CHB][hapmap];0.81[JPT][hapmap];0.91[ASN][1000 genomes]
rs334470	0.91[CEU][hapmap]
rs334473	0.80[EUR][1000 genomes]
rs334485	1.00[CEU][hapmap];0.93[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs334486	1.00[CEU][hapmap];0.93[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs334487	1.00[CEU][hapmap];0.93[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs334490	1.00[CEU][hapmap];0.92[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs334491	1.00[CEU][hapmap];0.93[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs334492	0.91[CEU][hapmap];0.85[JPT][hapmap];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs425779	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs595358	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs621932	0.93[JPT][hapmap]
rs6858960	1.00[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs899186	0.92[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs991891	0.92[CHB][hapmap];0.87[JPT][hapmap];0.94[ASN][1000 genomes]
rs994099	0.85[CHB][hapmap];0.81[JPT][hapmap];0.92[YRI][hapmap];0.93[ASN][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	nsv881187	chr5:16514269-16654960	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:16516000-16540800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr5:16521600-16539600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr5:16522400-16567400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr5:16523400-16540800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr5:16523600-16535400	Weak transcription	Pancreas	Pancrea
6	chr5:16523800-16539000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr5:16523800-16540800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr5:16525000-16540800	Weak transcription	Primary T helper cells PMA-I stimulated	--
9	chr5:16525000-16542000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr5:16525200-16540400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr5:16525600-16539200	Weak transcription	Gastric	stomach
12	chr5:16526400-16537400	Weak transcription	Primary T cells fromperipheralblood	blood
13	chr5:16527200-16534400	Weak transcription	Thymus	Thymus
14	chr5:16529000-16537000	Weak transcription	Fetal Brain Male	brain
15	chr5:16529000-16538000	Weak transcription	Fetal Brain Female	brain
16	chr5:16530400-16535400	Weak transcription	Right Atrium	heart
17	chr5:16530600-16535400	Weak transcription	Fetal Muscle Trunk	muscle
18	chr5:16531800-16536400	Weak transcription	Brain Anterior Caudate	brain
19	chr5:16532000-16534200	Weak transcription	Psoas Muscle	Psoas
20	chr5:16532000-16534400	Weak transcription	Fetal Muscle Leg	muscle
21	chr5:16532000-16534400	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr5:16532000-16535400	Weak transcription	Brain Hippocampus Middle	brain
23	chr5:16532000-16535600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr5:16532000-16538000	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr5:16532000-16538200	Weak transcription	Colonic Mucosa	Colon
26	chr5:16532000-16538200	Weak transcription	Fetal Intestine Large	intestine
27	chr5:16532200-16534400	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr5:16532200-16535400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
29	chr5:16532200-16535400	Weak transcription	Brain Cingulate Gyrus	brain
30	chr5:16532200-16535400	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr5:16532200-16535600	Weak transcription	Brain Angular Gyrus	brain
32	chr5:16532200-16536200	Weak transcription	Brain Substantia Nigra	brain
33	chr5:16532200-16536200	Weak transcription	Fetal Intestine Small	intestine
34	chr5:16532200-16538400	Weak transcription	Small Intestine	intestine
35	chr5:16532200-16542000	Weak transcription	Pancreatic Islets	Pancreatic Islet
36	chr5:16532400-16536000	Weak transcription	Duodenum Mucosa	Duodenum
37	chr5:16533200-16543200	Enhancers	Fetal Heart	heart
38	chr5:16533600-16539200	Weak transcription	Aorta	Aorta
39	chr5:16533800-16534200	Enhancers	Primary T helper cells fromperipheralblood	blood
40	chr5:16533800-16534200	Enhancers	Left Ventricle	heart
41	chr5:16533800-16534200	Enhancers	Right Ventricle	heart
42	chr5:16533800-16534600	Strong transcription	Primary T cells from cord blood	blood

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