Variant report

Variant	rs12099615
Chromosome Location	chr12:50958749-50958750
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:50947257..50949279-chr12:50958735..50961611,2	K562	blood:
2	chr12:50957129..50960260-chr12:50961650..50963740,3	K562	blood:
3	chr12:50957955..50959497-chr12:50959656..50962563,2	MCF-7	breast:
4	chr12:50951293..50953796-chr12:50956997..50959240,2	MCF-7	breast:
5	chr12:50950342..50953589-chr12:50956085..50960023,3	MCF-7	breast:

Extended variants
information (count: 124 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:123)

rs_ID	r²[population]
rs10506293	0.85[GIH][hapmap];0.85[TSI][hapmap];0.90[EUR][1000 genomes]
rs10506296	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];0.83[JPT][hapmap];0.95[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10735826	0.94[ASN][1000 genomes]
rs10783366	0.90[CHB][hapmap];0.95[JPT][hapmap]
rs10783367	0.92[ASN][1000 genomes]
rs10783368	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10876041	0.90[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs10876044	0.90[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs10876048	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10876054	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10876057	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10876082	1.00[CEU][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs10876083	0.86[EUR][1000 genomes]
rs10876088	0.86[EUR][1000 genomes]
rs11169422	0.90[EUR][1000 genomes]
rs11169551	1.00[CEU][hapmap];1.00[TSI][hapmap]
rs11169553	0.86[EUR][1000 genomes]
rs11614911	0.94[ASN][1000 genomes]
rs12099511	0.90[EUR][1000 genomes]
rs12296379	1.00[CEU][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12307602	0.90[EUR][1000 genomes]
rs12320201	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12817256	0.89[ASN][1000 genomes]
rs13328926	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1402693	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1521515	1.00[CEU][hapmap];0.85[CHB][hapmap];0.81[JPT][hapmap];0.86[EUR][1000 genomes]
rs1521517	1.00[CEU][hapmap];0.85[CHB][hapmap];0.94[GIH][hapmap];0.91[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs17119774	1.00[CEU][hapmap];0.85[GIH][hapmap];0.85[TSI][hapmap];0.90[EUR][1000 genomes]
rs17124672	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs17124888	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17124907	1.00[CEU][hapmap];0.85[CHB][hapmap];0.82[JPT][hapmap];0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17531020	1.00[CEU][hapmap]
rs1815010	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1996750	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2246840	1.00[CEU][hapmap];0.85[CHB][hapmap];0.83[JPT][hapmap];0.86[EUR][1000 genomes]
rs2252595	1.00[CEU][hapmap];0.84[CHB][hapmap];0.91[JPT][hapmap];0.91[EUR][1000 genomes]
rs2684886	0.86[EUR][1000 genomes]
rs2684890	1.00[CEU][hapmap];0.85[CHB][hapmap];0.82[JPT][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs2684891	1.00[CEU][hapmap];0.85[CHB][hapmap];0.83[JPT][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs2684902	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2684906	1.00[CEU][hapmap];0.85[CHB][hapmap];0.91[JPT][hapmap];0.95[EUR][1000 genomes]
rs2700486	0.86[EUR][1000 genomes]
rs28414775	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28479152	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2947617	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3803181	1.00[CEU][hapmap];0.85[CHB][hapmap];0.83[JPT][hapmap];0.82[YRI][hapmap];0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3825401	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4129355	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4132432	0.90[MEX][hapmap];0.82[AMR][1000 genomes]
rs4143663	1.00[CEU][hapmap];0.85[CHB][hapmap];0.82[JPT][hapmap];0.82[YRI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4257057	1.00[CEU][hapmap];0.85[GIH][hapmap];0.85[TSI][hapmap];0.90[EUR][1000 genomes]
rs4306347	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4450234	0.85[GIH][hapmap];0.85[TSI][hapmap];0.90[EUR][1000 genomes]
rs4517607	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4562889	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4768848	0.86[ASN][1000 genomes]
rs4768885	0.94[ASN][1000 genomes]
rs4768886	0.94[ASN][1000 genomes]
rs4768887	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4768894	0.94[ASN][1000 genomes]
rs4768915	0.82[JPT][hapmap];0.86[EUR][1000 genomes]
rs4768920	0.86[EUR][1000 genomes]
rs56671180	0.90[EUR][1000 genomes]
rs56753963	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56818625	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs57283487	0.90[EUR][1000 genomes]
rs57293958	0.90[EUR][1000 genomes]
rs57328764	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs57512759	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57578212	0.90[EUR][1000 genomes]
rs57811009	0.90[EUR][1000 genomes]
rs57828015	0.90[EUR][1000 genomes]
rs58301497	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs58500867	0.90[EUR][1000 genomes]
rs58869591	0.85[EUR][1000 genomes]
rs58888905	0.90[EUR][1000 genomes]
rs58915267	0.85[EUR][1000 genomes]
rs58916974	0.90[EUR][1000 genomes]
rs58943330	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59194948	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59284993	0.90[EUR][1000 genomes]
rs59683461	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59696942	0.90[EUR][1000 genomes]
rs59968707	0.90[EUR][1000 genomes]
rs60010359	0.90[EUR][1000 genomes]
rs60198651	0.90[EUR][1000 genomes]
rs60201334	0.90[EUR][1000 genomes]
rs60239257	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60242613	0.90[EUR][1000 genomes]
rs60396677	0.90[EUR][1000 genomes]
rs60420087	0.90[EUR][1000 genomes]
rs60494920	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60743903	0.90[EUR][1000 genomes]
rs60908906	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61578731	0.90[EUR][1000 genomes]
rs6580766	0.86[EUR][1000 genomes]
rs6580767	0.86[EUR][1000 genomes]
rs6580768	0.86[EUR][1000 genomes]
rs7131993	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7132443	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7135222	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7301125	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7302749	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7303202	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7304262	0.90[EUR][1000 genomes]
rs7306387	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7310507	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7487645	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7953880	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7955176	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs7955310	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7957060	0.88[ASN][1000 genomes]
rs7969251	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7974480	1.00[CEU][hapmap];0.85[GIH][hapmap];0.85[TSI][hapmap];0.90[EUR][1000 genomes]
rs7978443	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7979184	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7979474	1.00[CEU][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs865490	0.81[EUR][1000 genomes]
rs939631	1.00[CEU][hapmap];0.85[CHB][hapmap];0.82[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs951591	1.00[CEU][hapmap];0.85[CHB][hapmap];0.91[JPT][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9634264	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9738596	0.95[ASN][1000 genomes]
rs9804759	0.87[EUR][1000 genomes];0.88[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	esv1820967	chr12:50856613-51002088	Flanking Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:50920800-50962400	Weak transcription	Stomach Smooth Muscle	stomach
2	chr12:50927400-50961800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr12:50927800-50961800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr12:50932200-50961800	Weak transcription	Right Ventricle	heart
5	chr12:50936800-50962000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
6	chr12:50940000-50961400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr12:50940400-50961800	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr12:50940800-50962000	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr12:50941000-50961800	Weak transcription	Colon Smooth Muscle	Colon
10	chr12:50941000-50962000	Weak transcription	Brain Germinal Matrix	brain
11	chr12:50941000-50963000	Weak transcription	HSMMtube	muscle
12	chr12:50944400-50962000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr12:50944600-50961800	Weak transcription	Small Intestine	intestine
14	chr12:50944800-50961800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr12:50945200-50965200	Weak transcription	Fetal Muscle Trunk	muscle
16	chr12:50945400-50961800	Weak transcription	Esophagus	oesophagus
17	chr12:50945600-50958800	Weak transcription	Ovary	ovary
18	chr12:50947200-50961800	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr12:50947400-50958800	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr12:50948400-50966000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr12:50948800-50961400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr12:50949400-50961800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr12:50949400-50962000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr12:50949400-50962000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
25	chr12:50949400-50973600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr12:50949800-50962000	Weak transcription	Duodenum Mucosa	Duodenum
27	chr12:50949800-50962000	Weak transcription	Fetal Thymus	thymus
28	chr12:50950000-50961800	Weak transcription	Fetal Intestine Large	intestine
29	chr12:50951400-50961400	Weak transcription	Muscle Satellite Cultured Cells	--
30	chr12:50951600-50959200	Weak transcription	Dnd41	blood
31	chr12:50952000-50962000	Weak transcription	Fetal Intestine Small	intestine
32	chr12:50952000-50962000	Weak transcription	Fetal Stomach	stomach
33	chr12:50953400-50965600	Weak transcription	Primary B cells from cord blood	blood
34	chr12:50953800-50966000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr12:50954800-50959400	Enhancers	Liver	Liver
36	chr12:50955800-50960200	Enhancers	Primary hematopoietic stem cells short term culture	blood
37	chr12:50956200-50960000	Enhancers	HepG2	liver
38	chr12:50956200-50961000	Weak transcription	Stomach Mucosa	stomach
39	chr12:50956600-50958800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr12:50956600-50958800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr12:50956600-50961800	Weak transcription	Fetal Muscle Leg	muscle
42	chr12:50957000-50958800	Enhancers	Primary hematopoietic stem cells	blood
43	chr12:50957000-50959200	Enhancers	Primary monocytes fromperipheralblood	blood
44	chr12:50957200-50959200	Enhancers	Brain Substantia Nigra	brain
45	chr12:50957200-50965600	Weak transcription	Psoas Muscle	Psoas
46	chr12:50957400-50961800	Weak transcription	Left Ventricle	heart
47	chr12:50957600-50958800	Weak transcription	Spleen	Spleen
48	chr12:50957600-50959200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
49	chr12:50957600-50959200	Enhancers	Brain Inferior Temporal Lobe	brain
50	chr12:50957600-50959400	Enhancers	Brain Hippocampus Middle	brain

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