Variant report

Variant	rs10055964
Chromosome Location	chr5:127302816-127302817
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:127212523..127214164-chr5:127301948..127304809,2	MCF-7	breast:
2	chr5:127302540..127306473-chr5:127313949..127316469,3	MCF-7	breast:
3	chr5:127301710..127304376-chr5:127421505..127423068,2	MCF-7	breast:
4	chr5:127293170..127295868-chr5:127299899..127303794,5	MCF-7	breast:
5	chr5:127286727..127288267-chr5:127302316..127305106,2	MCF-7	breast:
6	chr5:127256203..127258500-chr5:127301825..127304365,2	MCF-7	breast:
7	chr5:127297981..127299833-chr5:127300238..127305210,4	MCF-7	breast:
8	chr5:127302253..127305011-chr5:127417884..127420763,3	MCF-7	breast:
9	chr5:127296445..127298165-chr5:127301266..127303118,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000245937	Chromatin interaction
ENSG00000064651	Chromatin interaction

Extended variants
information (count: 68 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10040931	0.89[CEU][hapmap];0.84[EUR][1000 genomes]
rs10041355	0.82[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs10041388	0.82[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs10052149	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10057048	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10059403	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.83[MKK][hapmap];0.98[TSI][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10076010	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10463835	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10463836	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10478786	0.87[EUR][1000 genomes]
rs10478787	0.92[CEU][hapmap];0.97[LWK][hapmap];0.88[MKK][hapmap];0.93[TSI][hapmap];0.92[YRI][hapmap];0.91[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs10478788	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10478790	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10478791	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10478792	0.92[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10519968	0.92[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10519977	0.92[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.84[GIH][hapmap];0.94[JPT][hapmap];0.83[MKK][hapmap];0.93[TSI][hapmap];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11745009	0.92[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs11745023	0.88[CEU][hapmap];0.84[EUR][1000 genomes]
rs12523625	0.92[CEU][hapmap];0.93[TSI][hapmap];0.87[EUR][1000 genomes]
rs13154863	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13161109	0.93[EUR][1000 genomes]
rs13167871	0.94[CHB][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs13169878	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13174053	0.81[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs13177354	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13180050	0.83[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs13184942	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1558149	0.92[CEU][hapmap];0.91[TSI][hapmap];0.87[EUR][1000 genomes]
rs17606751	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2041143	0.89[CEU][hapmap]
rs2108652	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2108654	0.82[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs2159110	0.82[EUR][1000 genomes]
rs2409038	0.86[EUR][1000 genomes]
rs2409039	0.85[EUR][1000 genomes]
rs2409040	0.82[EUR][1000 genomes]
rs2898077	0.85[EUR][1000 genomes]
rs34498802	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35673135	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35713319	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4835934	0.86[EUR][1000 genomes]
rs4836352	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4836354	0.82[ASN][1000 genomes]
rs5008451	0.96[CEU][hapmap]
rs59634534	0.83[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs6867103	0.95[CEU][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6867442	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6867465	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6867644	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6881456	0.86[EUR][1000 genomes]
rs6889393	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6892704	0.92[CEU][hapmap];0.91[TSI][hapmap];0.86[EUR][1000 genomes]
rs6897353	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs732235	0.86[EUR][1000 genomes]
rs732236	0.92[CEU][hapmap];0.81[LWK][hapmap];0.80[MKK][hapmap];0.93[TSI][hapmap];0.92[YRI][hapmap];0.83[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs7444438	0.87[AFR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs768528	0.81[EUR][1000 genomes]
rs7711776	1.00[ASW][hapmap];0.92[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.84[GIH][hapmap];0.88[JPT][hapmap];0.85[LWK][hapmap];0.88[MKK][hapmap];0.93[TSI][hapmap];0.91[YRI][hapmap];0.92[AFR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7717705	0.80[EUR][1000 genomes]
rs7719691	0.88[CHB][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs7732912	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9327458	0.83[YRI][hapmap]
rs9327460	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9327461	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9327462	0.92[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.84[GIH][hapmap];0.94[JPT][hapmap];0.82[MKK][hapmap];0.93[TSI][hapmap];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1033607	chr5:126385181-127304459	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv1021483	chr5:126927834-127304873	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10055964	SLC12A2	cis	cerebellum	SCAN

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:127285800-127303800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
2	chr5:127290600-127332000	Weak transcription	Aorta	Aorta
3	chr5:127292800-127314400	Weak transcription	Pancreas	Pancrea
4	chr5:127293200-127303600	Weak transcription	Esophagus	oesophagus
5	chr5:127295600-127304400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr5:127295800-127322800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr5:127296200-127303000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr5:127296200-127303800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr5:127296200-127304800	Weak transcription	Brain Substantia Nigra	brain
10	chr5:127296200-127306000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr5:127296200-127307200	Weak transcription	NHLF	lung
12	chr5:127296200-127322600	Weak transcription	Colon Smooth Muscle	Colon
13	chr5:127296400-127303000	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr5:127296400-127303800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr5:127296400-127304000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr5:127296400-127304200	Weak transcription	Primary T helper cells fromperipheralblood	blood
17	chr5:127296400-127304800	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr5:127296400-127304800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr5:127296400-127305200	Weak transcription	Brain Anterior Caudate	brain
20	chr5:127296400-127306400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr5:127297000-127305200	Weak transcription	Brain Hippocampus Middle	brain
22	chr5:127297600-127303000	Weak transcription	Thymus	Thymus
23	chr5:127297600-127304600	Weak transcription	Stomach Smooth Muscle	stomach
24	chr5:127297600-127313200	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr5:127297600-127332000	Weak transcription	Primary B cells from cord blood	blood
26	chr5:127297800-127304000	Weak transcription	Primary B cells from peripheral blood	blood
27	chr5:127297800-127306400	Weak transcription	Psoas Muscle	Psoas
28	chr5:127297800-127306400	Weak transcription	Right Atrium	heart
29	chr5:127297800-127323200	Weak transcription	Gastric	stomach
30	chr5:127297800-127323600	Weak transcription	HSMMtube	muscle
31	chr5:127297800-127358400	Weak transcription	Primary hematopoietic stem cells	blood
32	chr5:127298000-127304000	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr5:127298400-127303400	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr5:127298400-127303800	Weak transcription	Rectal Mucosa Donor 29	rectum
35	chr5:127298400-127304800	Weak transcription	Small Intestine	intestine
36	chr5:127298600-127314400	Weak transcription	Duodenum Mucosa	Duodenum
37	chr5:127299400-127303800	Weak transcription	NHDF-Ad	bronchial
38	chr5:127300600-127312600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr5:127301800-127303200	Strong transcription	Primary T cells from cord blood	blood
40	chr5:127302000-127304200	Enhancers	Stomach Mucosa	stomach
41	chr5:127302200-127304000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr5:127302200-127304800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr5:127302400-127304200	Enhancers	A549	lung
44	chr5:127302400-127304800	Weak transcription	Right Ventricle	heart
45	chr5:127302400-127306800	Weak transcription	GM12878-XiMat	blood
46	chr5:127302400-127307000	Weak transcription	Ovary	ovary
47	chr5:127302400-127321600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr5:127302400-127323400	Weak transcription	Fetal Stomach	stomach
49	chr5:127302600-127304200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
50	chr5:127302600-127305800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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