Variant report

Variant	rs11168797
Chromosome Location	chr12:49338841-49338842
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:49329355..49335445-chr12:49337368..49342700,9	MCF-7	breast:
2	chr12:49338699..49342027-chr12:49368577..49371110,3	MCF-7	breast:
3	chr12:49335548..49339838-chr12:49342673..49348492,5	K562	blood:
4	chr12:49334719..49339630-chr12:49347637..49352407,8	MCF-7	breast:
5	chr12:49338507..49340328-chr12:49351124..49352649,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000134287	Chromatin interaction
ENSG00000272822	Chromatin interaction
ENSG00000255863	Chromatin interaction
ENSG00000200303	Chromatin interaction

Extended variants
information (count: 123 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:119)

rs_ID	r²[population]
rs1051886	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1054376	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10747556	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10747557	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10747558	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10783289	0.90[ASN][1000 genomes]
rs10783290	0.87[ASN][1000 genomes]
rs10783292	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10783293	0.92[ASN][1000 genomes]
rs10783294	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10783295	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10783297	0.82[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs10875886	0.92[ASN][1000 genomes]
rs10875888	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10875893	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10875894	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10875895	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10875896	0.81[AFR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10875897	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10875898	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10875899	0.84[ASN][1000 genomes]
rs10875900	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10875901	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10875902	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1111662	1.00[ASN][1000 genomes]
rs11168779	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11168783	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11168784	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11168785	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11168790	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11168792	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11168794	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11168795	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11168798	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11168800	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11168801	0.93[ASN][1000 genomes]
rs11168803	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11168811	0.86[ASN][1000 genomes]
rs11168812	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11608916	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11610459	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11610497	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11614474	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12227240	0.87[AFR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12228521	0.85[AFR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12229275	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12423542	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12579249	0.92[ASN][1000 genomes]
rs1318692	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1690182	0.97[ASN][1000 genomes]
rs1818996	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1830192	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2030900	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2070940	0.97[ASN][1000 genomes]
rs2073480	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2131713	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2272311	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2272312	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2293449	0.93[ASN][1000 genomes]
rs2368701	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2453063	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2463175	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2641450	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2694839	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2694840	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3741627	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3759146	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3782353	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3809147	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3825182	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3825184	0.91[ASN][1000 genomes]
rs4018510	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4237854	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4433614	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4526804	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4760600	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4760647	0.86[EUR][1000 genomes]
rs4760661	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4760662	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4760663	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4760664	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4760665	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4760666	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4760667	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4760668	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58023472	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs59087236	0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61941142	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61942166	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61942167	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61942169	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61942207	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61942209	0.87[ASN][1000 genomes]
rs6580696	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7297958	0.92[ASN][1000 genomes]
rs7298330	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7304942	0.92[ASN][1000 genomes]
rs7313988	0.98[ASN][1000 genomes]
rs7489036	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7963018	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7963160	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7976473	0.92[ASN][1000 genomes]
rs833820	0.96[ASN][1000 genomes]
rs833821	0.96[ASN][1000 genomes]
rs833822	0.98[ASN][1000 genomes]
rs833827	0.98[ASN][1000 genomes]
rs833828	0.96[ASN][1000 genomes]
rs833839	0.88[ASN][1000 genomes]
rs833840	0.88[ASN][1000 genomes]
rs833841	0.88[ASN][1000 genomes]
rs833842	0.88[ASN][1000 genomes]
rs833843	0.85[ASN][1000 genomes]
rs961320	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9645813	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9783452	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9783477	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9788029	0.94[ASN][1000 genomes]
rs9795742	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9796008	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]

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	nsv832404	chr12:49258560-49458555	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	nsv1051161	chr12:49314550-49828473	Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Active TSS Strong transcription Enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
3	nsv541489	chr12:49314550-49828473	Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
4	nsv899067	chr12:49329695-49344508	Enhancers Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11168797	RP11-302B13.1	cis	Whole Blood	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:49319200-49349800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr12:49319800-49349400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr12:49329400-49349400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
4	chr12:49330200-49339400	Weak transcription	Fetal Brain Male	brain
5	chr12:49330600-49341400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr12:49330800-49349000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr12:49332000-49349000	Weak transcription	Stomach Mucosa	stomach
8	chr12:49333800-49349400	Weak transcription	Rectal Smooth Muscle	rectum
9	chr12:49334200-49346200	Weak transcription	Fetal Kidney	kidney
10	chr12:49334600-49342200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr12:49334800-49339800	Weak transcription	Right Atrium	heart
12	chr12:49334800-49340600	Weak transcription	Fetal Lung	lung
13	chr12:49334800-49342600	Weak transcription	K562	blood
14	chr12:49334800-49343600	Weak transcription	Primary B cells from peripheral blood	blood
15	chr12:49334800-49346000	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr12:49334800-49346400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr12:49334800-49348000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr12:49334800-49348600	Weak transcription	Small Intestine	intestine
19	chr12:49334800-49349400	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr12:49334800-49349800	Weak transcription	Psoas Muscle	Psoas
21	chr12:49335000-49340000	Weak transcription	Brain Anterior Caudate	brain
22	chr12:49335000-49340400	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr12:49335000-49342200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
24	chr12:49335000-49346200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr12:49335000-49346600	Weak transcription	Ovary	ovary
26	chr12:49335000-49349400	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr12:49335000-49349800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr12:49335200-49339800	Weak transcription	Brain Angular Gyrus	brain
29	chr12:49335200-49339800	Weak transcription	Rectal Mucosa Donor 31	rectum
30	chr12:49335200-49340000	Weak transcription	Primary hematopoietic stem cells	blood
31	chr12:49335200-49340000	Weak transcription	Pancreas	Pancrea
32	chr12:49335200-49340200	Weak transcription	Brain Cingulate Gyrus	brain
33	chr12:49335200-49340400	Weak transcription	Gastric	stomach
34	chr12:49335200-49340400	Weak transcription	Right Ventricle	heart
35	chr12:49335200-49340600	Weak transcription	HSMM	muscle
36	chr12:49335200-49346000	Weak transcription	NH-A	brain
37	chr12:49335200-49346200	Weak transcription	H1 Cell Line	embryonic stem cell
38	chr12:49335200-49346200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
39	chr12:49335200-49346400	Weak transcription	Aorta	Aorta
40	chr12:49335200-49349600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr12:49335400-49340400	Weak transcription	Lung	lung
42	chr12:49335400-49340600	Weak transcription	Colon Smooth Muscle	Colon
43	chr12:49335400-49345800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr12:49335400-49349000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
45	chr12:49335400-49349400	Weak transcription	Liver	Liver
46	chr12:49335400-49349800	Weak transcription	Spleen	Spleen
47	chr12:49335600-49339400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr12:49335600-49340000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
49	chr12:49335600-49340000	Weak transcription	Cortex derived primary cultured neurospheres	brain
50	chr12:49335800-49339800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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