Variant report

Variant	rs1152896
Chromosome Location	chr12:67683663-67683664
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:67681823..67684693-chr12:67719727..67722113,2	K562	blood:
2	chr12:67682602..67685085-chr12:67687619..67689287,2	K562	blood:
3	chr12:67662696..67664703-chr12:67682661..67684692,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000111530	Chromatin interaction

Extended variants
information (count: 125 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:121)

rs_ID	r²[population]
rs10506544	0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1060350	1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1066387	0.93[GIH][hapmap]
rs1066389	0.98[ASN][1000 genomes]
rs1066390	0.98[ASN][1000 genomes]
rs1066391	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1066396	0.98[ASN][1000 genomes]
rs1066398	0.98[ASN][1000 genomes]
rs1066399	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1066404	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10784619	0.97[ASN][1000 genomes]
rs10784624	0.83[ASN][1000 genomes]
rs10784625	0.89[GIH][hapmap];0.83[MEX][hapmap]
rs1082700	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1082710	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10878596	1.00[ASN][1000 genomes]
rs10878601	0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs1092600	0.98[ASN][1000 genomes]
rs1112445	0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs11176647	0.93[ASN][1000 genomes]
rs11176657	0.93[ASN][1000 genomes]
rs11176677	0.98[ASN][1000 genomes]
rs11176678	0.93[GIH][hapmap]
rs11176683	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs11176690	0.93[ASN][1000 genomes]
rs11176695	0.92[ASN][1000 genomes]
rs11176700	0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs1125748	0.81[ASN][1000 genomes]
rs1136080	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1137465	0.98[ASN][1000 genomes]
rs1143954	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1143956	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1144939	0.95[ASN][1000 genomes]
rs1152877	0.89[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1152895	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1152897	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1152898	0.96[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];0.98[ASN][1000 genomes]
rs1152901	0.96[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];0.98[ASN][1000 genomes]
rs1152902	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1161085	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1161087	0.89[ASN][1000 genomes]
rs1161089	0.98[ASN][1000 genomes]
rs1161090	0.98[ASN][1000 genomes]
rs1161092	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1183126	0.95[ASN][1000 genomes]
rs1184743	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1185918	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12366819	0.98[ASN][1000 genomes]
rs12369715	0.92[ASN][1000 genomes]
rs12370954	0.97[ASN][1000 genomes]
rs12422358	0.92[ASN][1000 genomes]
rs12422968	0.98[ASN][1000 genomes]
rs12424158	1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.98[ASN][1000 genomes]
rs1252364	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1252386	0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1252387	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1252388	0.94[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1252402	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[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];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1252405	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1252407	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1252419	1.00[ASN][1000 genomes]
rs1252422	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1252424	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12580790	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1272089	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1392587	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1500431	0.93[ASN][1000 genomes]
rs1561333	0.81[ASN][1000 genomes]
rs1583648	0.93[ASN][1000 genomes]
rs1612693	0.93[ASN][1000 genomes]
rs1697232	0.98[ASN][1000 genomes]
rs1697233	1.00[CEU][hapmap];0.95[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]
rs17781745	0.95[ASN][1000 genomes]
rs1921000	0.89[ASN][1000 genomes]
rs1985476	0.90[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2028213	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2091698	0.97[ASN][1000 genomes]
rs2118311	0.93[ASN][1000 genomes]
rs2118533	0.81[ASN][1000 genomes]
rs2178466	0.84[ASN][1000 genomes]
rs2248751	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2438109	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2576941	1.00[ASN][1000 genomes]
rs3736630	0.87[YRI][hapmap]
rs3861890	0.97[ASN][1000 genomes]
rs4913538	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4913540	0.98[ASN][1000 genomes]
rs4913541	0.93[ASN][1000 genomes]
rs61918267	0.99[ASN][1000 genomes]
rs61920672	0.98[ASN][1000 genomes]
rs698123	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.96[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs710626	0.97[ASN][1000 genomes]
rs710627	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs710628	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs710629	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs710630	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs710800	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7134743	0.92[ASN][1000 genomes]
rs775306	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs775309	1.00[ASN][1000 genomes]
rs775310	0.93[GIH][hapmap]
rs775312	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs775628	0.93[GIH][hapmap]
rs775644	0.93[ASN][1000 genomes]
rs775645	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs775651	0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs775652	0.89[ASN][1000 genomes]
rs775655	0.89[ASN][1000 genomes]
rs775660	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];0.97[ASN][1000 genomes]
rs775662	0.93[GIH][hapmap]
rs796522	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7968645	0.98[ASN][1000 genomes]
rs7973565	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7977430	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs800166	0.93[GIH][hapmap]
rs811820	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs811827	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs812325	0.93[GIH][hapmap]
rs812326	0.93[GIH][hapmap]
rs814290	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs983630	0.93[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv541524	chr12:67311057-67700349	Strong transcription Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv559212	chr12:67373549-67850925	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv1054111	chr12:67556780-67865542	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer 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	20 gene(s)	inside rSNPs	diseases
4	nsv525023	chr12:67672870-67708669	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS	TF binding region Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1152896	YEATS4	cis	cerebellum	SCAN
rs1152896	RASSF3	cis	cerebellum	SCAN
rs1152896	DYRK2	cis	cerebellum	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:67664600-67684000	Weak transcription	Fetal Muscle Trunk	muscle
2	chr12:67664800-67694400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr12:67664800-67699600	Weak transcription	Aorta	Aorta
4	chr12:67665200-67684400	Weak transcription	Fetal Muscle Leg	muscle
5	chr12:67665200-67684600	Weak transcription	Thymus	Thymus
6	chr12:67665200-67690200	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr12:67665200-67699000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr12:67665400-67687600	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr12:67666000-67688400	Weak transcription	Fetal Kidney	kidney
10	chr12:67666000-67701000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr12:67668400-67688200	Weak transcription	HUVEC	blood vessel
12	chr12:67670000-67684200	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr12:67670000-67688800	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr12:67670000-67699200	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr12:67670200-67698200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr12:67670400-67689600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr12:67670600-67684400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr12:67670800-67688400	Weak transcription	Rectal Smooth Muscle	rectum
19	chr12:67671000-67688800	Weak transcription	NHEK	skin
20	chr12:67671000-67689400	Weak transcription	NHLF	lung
21	chr12:67671200-67688200	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr12:67671400-67698400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr12:67671600-67691800	Weak transcription	Fetal Brain Male	brain
24	chr12:67672200-67699000	Weak transcription	Esophagus	oesophagus
25	chr12:67672400-67684600	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr12:67672400-67693800	Weak transcription	Psoas Muscle	Psoas
27	chr12:67672600-67684600	Weak transcription	Gastric	stomach
28	chr12:67672600-67684600	Weak transcription	Right Atrium	heart
29	chr12:67673200-67699400	Weak transcription	Small Intestine	intestine
30	chr12:67674200-67684600	Weak transcription	Brain Anterior Caudate	brain
31	chr12:67674200-67688800	Weak transcription	Brain Angular Gyrus	brain
32	chr12:67674200-67694000	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr12:67674400-67684600	Weak transcription	Fetal Lung	lung
34	chr12:67674400-67696000	Weak transcription	Brain Hippocampus Middle	brain
35	chr12:67674600-67689800	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr12:67674600-67708000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr12:67674800-67697800	Strong transcription	Fetal Thymus	thymus
38	chr12:67674800-67706400	Weak transcription	Stomach Mucosa	stomach
39	chr12:67675400-67685400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr12:67675600-67685200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr12:67675600-67694600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr12:67675800-67685600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr12:67676200-67691000	Weak transcription	HMEC	breast
44	chr12:67676600-67685000	Strong transcription	A549	lung
45	chr12:67676800-67691800	Weak transcription	Primary neutrophils fromperipheralblood	blood
46	chr12:67677400-67684600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr12:67677600-67684400	Weak transcription	Brain Germinal Matrix	brain
48	chr12:67678600-67684200	Weak transcription	Liver	Liver
49	chr12:67678600-67699000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr12:67678800-67684200	Weak transcription	HSMMtube	muscle

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