Variant report

Variant	rs12825507
Chromosome Location	chr12:9844581-9844582
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:9843930-9845980	GM12892	blood:	n/a	n/a
2	POLR2A	chr12:9844508-9845245	GM12892	blood:	n/a	n/a
3	POLR2A	chr12:9844527-9844656	MCF10A-Er-Src	breast:	n/a	n/a
4	POLR2A	chr12:9844518-9845234	GM12892	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:9801129..9802680-chr12:9843178..9846016,2	K562	blood:
2	chr12:9811398..9813621-chr12:9843826..9845661,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000213443	TF binding region

Extended variants
information (count: 127 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:125)

rs_ID	r²[population]
rs1008611	1.00[CEU][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs10466762	1.00[JPT][hapmap]
rs10743820	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs10743821	1.00[CEU][hapmap];0.84[ASN][1000 genomes]
rs10743822	1.00[CEU][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs10772005	1.00[JPT][hapmap]
rs10772006	1.00[JPT][hapmap]
rs10772060	1.00[CHB][hapmap]
rs10772104	1.00[JPT][hapmap]
rs10772119	1.00[JPT][hapmap]
rs10772120	1.00[JPT][hapmap]
rs10844350	1.00[JPT][hapmap]
rs10844351	1.00[JPT][hapmap]
rs10844359	1.00[JPT][hapmap]
rs10844372	1.00[JPT][hapmap]
rs10844418	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10844424	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[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10844429	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.92[TSI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10844449	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10844457	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10844476	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10844780	1.00[JPT][hapmap]
rs11052234	1.00[JPT][hapmap];1.00[LWK][hapmap];0.85[MEX][hapmap]
rs11052241	1.00[JPT][hapmap]
rs11052254	1.00[JPT][hapmap]
rs11052303	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11052304	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11052305	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11052311	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11052327	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11052342	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11052366	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11052367	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11052430	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[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11052431	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[GIH][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11052434	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11052718	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs11052785	0.84[ASN][1000 genomes]
rs11053051	1.00[JPT][hapmap]
rs11519377	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11524523	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12309762	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12320830	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12366653	1.00[JPT][hapmap];1.00[LWK][hapmap];0.85[MEX][hapmap]
rs12368445	0.90[CEU][hapmap];1.00[JPT][hapmap]
rs12371981	1.00[CHD][hapmap];0.83[GIH][hapmap]
rs12371982	1.00[AFR][1000 genomes]
rs12578698	0.84[ASN][1000 genomes]
rs12578928	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12582616	1.00[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs12810851	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12812783	1.00[AFR][1000 genomes]
rs12815393	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12817365	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12823653	1.00[CHB][hapmap]
rs12823699	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12824491	1.00[JPT][hapmap]
rs12828602	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12828773	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12830419	1.00[JPT][hapmap]
rs12831453	1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1560008	1.00[JPT][hapmap]
rs16913477	1.00[JPT][hapmap]
rs1861089	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap]
rs1863871	1.00[JPT][hapmap]
rs1990533	1.00[CEU][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2080207	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap]
rs2114869	1.00[JPT][hapmap]
rs2114872	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2114873	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2192433	0.84[ASN][1000 genomes]
rs2192434	0.84[ASN][1000 genomes]
rs2192435	0.84[ASN][1000 genomes]
rs2192439	0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2401396	1.00[CEU][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2401397	1.00[JPT][hapmap]
rs2401398	1.00[JPT][hapmap]
rs3176792	0.90[CEU][hapmap]
rs3176800	1.00[JPT][hapmap]
rs3176802	1.00[JPT][hapmap]
rs3176806	1.00[JPT][hapmap]
rs34201389	0.87[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs34850016	0.89[AFR][1000 genomes]
rs35210729	0.86[AMR][1000 genomes]
rs35237063	1.00[AFR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4763264	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4763813	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap]
rs4763814	1.00[CHB][hapmap]
rs4763835	0.84[ASN][1000 genomes]
rs61913428	0.87[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs6416258	1.00[JPT][hapmap]
rs6488065	1.00[JPT][hapmap]
rs6488109	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6488122	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs704223	1.00[JPT][hapmap]
rs7132037	1.00[JPT][hapmap]
rs7302110	1.00[JPT][hapmap]
rs7302746	1.00[JPT][hapmap]
rs7304321	1.00[JPT][hapmap]
rs7304464	1.00[JPT][hapmap]
rs7309800	1.00[JPT][hapmap]
rs7310568	1.00[JPT][hapmap]
rs7310790	1.00[JPT][hapmap]
rs7310897	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7311421	1.00[JPT][hapmap]
rs7311574	1.00[JPT][hapmap]
rs7311945	1.00[JPT][hapmap]
rs7312624	1.00[JPT][hapmap]
rs7485402	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap]
rs7954062	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7961416	1.00[JPT][hapmap];1.00[LWK][hapmap];0.85[MEX][hapmap]
rs7961812	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs7962321	1.00[JPT][hapmap]
rs7969074	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7972035	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7974871	1.00[JPT][hapmap]
rs7975557	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap]
rs7978187	1.00[JPT][hapmap]
rs7979758	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs929615	1.00[JPT][hapmap]
rs9630264	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9630265	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9668568	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs982511	1.00[CEU][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.84[ASN][1000 genomes]
rs9919786	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	esv2758293	chr12:9371595-9923529	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	40 gene(s)	inside rSNPs	diseases
2	esv2759878	chr12:9371595-9923529	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12825507	LOC374443	Cis_1M	lymphoblastoid	RTeQTL
rs12825507	CD69	cis	cerebellum	SCAN
rs12825507	PRB4	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:9802400-9849800	Weak transcription	Pancreas	Pancrea
2	chr12:9807600-9847200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr12:9818000-9849800	Weak transcription	Brain Germinal Matrix	brain
4	chr12:9826400-9849000	Weak transcription	Psoas Muscle	Psoas
5	chr12:9826600-9847200	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr12:9826600-9852400	Weak transcription	Colon Smooth Muscle	Colon
7	chr12:9826800-9844600	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr12:9826800-9848400	Weak transcription	Colonic Mucosa	Colon
9	chr12:9826800-9849400	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr12:9826800-9849800	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr12:9826800-9854400	Weak transcription	Esophagus	oesophagus
12	chr12:9827000-9853200	Weak transcription	Rectal Smooth Muscle	rectum
13	chr12:9827200-9847000	Weak transcription	NH-A	brain
14	chr12:9827200-9847400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr12:9827200-9847600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr12:9827200-9851000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr12:9827200-9851600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr12:9827200-9852400	Weak transcription	Osteobl	bone
19	chr12:9827400-9849000	Weak transcription	A549	lung
20	chr12:9832800-9846000	Weak transcription	Gastric	stomach
21	chr12:9833000-9849000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr12:9833200-9847200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr12:9835400-9849200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr12:9835800-9847000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr12:9837000-9847400	Weak transcription	Fetal Brain Female	brain
26	chr12:9837800-9846800	Strong transcription	Primary neutrophils fromperipheralblood	blood
27	chr12:9837800-9849400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr12:9838200-9849800	Strong transcription	Fetal Thymus	thymus
29	chr12:9838400-9844800	Weak transcription	Left Ventricle	heart
30	chr12:9838400-9849600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr12:9838800-9846200	Strong transcription	Primary monocytes fromperipheralblood	blood
32	chr12:9838800-9849200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
33	chr12:9838800-9854400	Weak transcription	Spleen	Spleen
34	chr12:9839000-9854400	Weak transcription	Lung	lung
35	chr12:9839400-9848800	Weak transcription	Brain Substantia Nigra	brain
36	chr12:9839400-9854600	Weak transcription	Small Intestine	intestine
37	chr12:9839600-9846200	Weak transcription	HepG2	liver
38	chr12:9840000-9849000	Weak transcription	H9 Cell Line	embryonic stem cell
39	chr12:9840200-9848200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
40	chr12:9840400-9847000	Weak transcription	Ovary	ovary
41	chr12:9840400-9847800	Weak transcription	Aorta	Aorta
42	chr12:9840600-9848400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr12:9840600-9864600	Weak transcription	Placenta Amnion	Placenta Amnion
44	chr12:9840800-9847800	Strong transcription	Primary B cells from peripheral blood	blood
45	chr12:9841000-9845600	Weak transcription	Stomach Smooth Muscle	stomach
46	chr12:9841000-9849600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
47	chr12:9841200-9844800	Strong transcription	Primary T cells fromperipheralblood	blood
48	chr12:9841200-9847600	Weak transcription	Fetal Intestine Small	intestine
49	chr12:9841200-9847800	Weak transcription	Thymus	Thymus
50	chr12:9841800-9844600	Weak transcription	Sigmoid Colon	Sigmoid Colon

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