Variant report

Variant	rs12900244
Chromosome Location	chr15:57018845-57018846
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:56999178..57001451-chr15:57017169..57019734,2	K562	blood:

Variant related genes	Relation type
ENSG00000137871	Chromatin interaction

Extended variants
information (count: 91 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs1010700	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10518870	0.88[CEU][hapmap];0.84[EUR][1000 genomes]
rs11071287	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11071293	0.83[EUR][1000 genomes]
rs11630168	0.96[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap]
rs11632471	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11633363	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11635333	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11638497	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11638580	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11638707	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11852277	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11856558	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.85[YRI][hapmap];0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11857388	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11857706	0.93[CEU][hapmap];0.95[CHB][hapmap];0.96[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs12438709	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12442018	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12442189	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap]
rs12591502	1.00[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.94[YRI][hapmap];0.81[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs12592389	0.96[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap]
rs12593286	0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12595822	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12898521	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12898760	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12900045	0.81[EUR][1000 genomes]
rs12900441	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12901887	0.82[CEU][hapmap]
rs12903283	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs12903336	0.92[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap]
rs12903862	0.92[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs12905514	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12906591	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12906830	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12908806	0.81[EUR][1000 genomes]
rs12908906	0.80[AMR][1000 genomes]
rs12910403	0.80[EUR][1000 genomes]
rs12910442	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12910459	0.89[CEU][hapmap];0.84[EUR][1000 genomes]
rs12911191	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12911381	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12912666	0.96[CEU][hapmap];0.88[EUR][1000 genomes]
rs12913361	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12913871	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12913960	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12915816	0.81[EUR][1000 genomes]
rs12916079	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1424694	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1477475	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs16977020	0.85[CHB][hapmap];0.82[JPT][hapmap]
rs17238845	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs1812395	0.82[EUR][1000 genomes]
rs1895640	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1979467	0.92[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1994081	0.96[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap]
rs2052640	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2161934	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2170459	0.89[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap]
rs2170463	0.88[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap]
rs2279298	1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.94[YRI][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2279299	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2414480	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28620278	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3803457	0.92[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs3816752	0.80[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3929265	0.88[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap]
rs4601984	0.82[EUR][1000 genomes]
rs4774244	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4774884	0.80[AMR][1000 genomes]
rs4774886	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs521904	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs538382	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs553421	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs559736	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs57387969	0.89[EUR][1000 genomes]
rs62022931	0.91[EUR][1000 genomes]
rs62022933	0.88[EUR][1000 genomes]
rs62022934	0.89[EUR][1000 genomes]
rs6493885	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7162317	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7165831	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7168178	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7169454	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7178796	0.80[AMR][1000 genomes]
rs7182187	0.80[AMR][1000 genomes]
rs795032	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8025391	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8036217	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8041540	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8043223	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]

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	esv3422474	chr15:56867190-57244330	Strong transcription ZNF genes & repeats Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
2	nsv569576	chr15:57012816-57126917	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:56958400-57019200	Weak transcription	Fetal Intestine Small	intestine
2	chr15:56971000-57023400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr15:56992400-57021800	Weak transcription	Right Ventricle	heart
4	chr15:56992600-57022600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr15:56993000-57024000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr15:56993400-57021600	Weak transcription	Fetal Brain Male	brain
7	chr15:56994000-57023800	Weak transcription	Fetal Kidney	kidney
8	chr15:56995800-57022200	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr15:56996000-57021800	Weak transcription	Rectal Smooth Muscle	rectum
10	chr15:56996400-57021600	Weak transcription	HSMMtube	muscle
11	chr15:56996400-57022600	Weak transcription	NH-A	brain
12	chr15:56996800-57022600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr15:56997200-57022800	Weak transcription	Gastric	stomach
14	chr15:56997200-57023800	Weak transcription	Fetal Stomach	stomach
15	chr15:56998400-57021200	Weak transcription	Stomach Smooth Muscle	stomach
16	chr15:56998800-57021800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr15:56998800-57023400	Weak transcription	Primary T cells fromperipheralblood	blood
18	chr15:56998800-57023800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr15:56999400-57023400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr15:57009200-57021400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr15:57009400-57022800	Weak transcription	Right Atrium	heart
22	chr15:57009400-57024400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr15:57011000-57022200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr15:57011200-57022600	Weak transcription	Fetal Heart	heart
25	chr15:57011400-57021200	Weak transcription	Brain Substantia Nigra	brain
26	chr15:57011400-57021400	Weak transcription	Adipose Nuclei	Adipose
27	chr15:57011400-57021800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr15:57011600-57021000	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr15:57011600-57022600	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr15:57011600-57023400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr15:57011600-57024400	Weak transcription	H1 Cell Line	embryonic stem cell
32	chr15:57011600-57024400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr15:57011800-57019200	Weak transcription	Primary monocytes fromperipheralblood	blood
34	chr15:57011800-57022600	Weak transcription	HMEC	breast
35	chr15:57011800-57024000	Weak transcription	Aorta	Aorta
36	chr15:57012400-57022600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr15:57012400-57022600	Weak transcription	Osteobl	bone
38	chr15:57012400-57025000	Weak transcription	Spleen	Spleen
39	chr15:57012600-57022600	Weak transcription	NHEK	skin
40	chr15:57012600-57023000	Weak transcription	NHLF	lung
41	chr15:57012600-57023400	Weak transcription	Psoas Muscle	Psoas
42	chr15:57013000-57022800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr15:57013200-57022600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr15:57013400-57024200	Weak transcription	Ovary	ovary
45	chr15:57014000-57022400	Weak transcription	Brain Germinal Matrix	brain
46	chr15:57014200-57022800	Weak transcription	K562	blood
47	chr15:57014800-57019200	Weak transcription	A549	lung
48	chr15:57015400-57022600	Weak transcription	HUVEC	blood vessel
49	chr15:57015800-57019200	Enhancers	Primary T helper naive cells from peripheral blood	blood
50	chr15:57016000-57019000	Enhancers	Primary T killer naive cells fromperipheralblood	blood

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