Variant report

Variant	rs11169140
Chromosome Location	chr12:50141447-50141448
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:16)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:16 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:50141319-50141499	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr12:50141254-50141843	MCF10A-Er-Src	breast:	n/a	n/a
3	POLR2A	chr12:50141375-50141825	GM12892	blood:	n/a	n/a
4	POLR2A	chr12:50141426-50141682	HepG2	liver:	n/a	n/a
5	POLR2A	chr12:50140801-50141821	GM12878	blood:	n/a	n/a
6	POLR2A	chr12:50141280-50141457	MCF-7	breast:	n/a	n/a
7	POLR2A	chr12:50140846-50143188	A549	lung:	n/a	n/a
8	POLR2A	chr12:50140974-50141741	GM12892	blood:	n/a	n/a
9	POLR2A	chr12:50141428-50141726	K562	blood:	n/a	n/a
10	POLR2A	chr12:50140746-50141813	Hela-S3	cervix:	n/a	n/a
11	POLR2A	chr12:50141370-50141886	GM12891	blood:	n/a	n/a
12	POLR2A	chr12:50141405-50141703	GM12878	blood:	n/a	n/a
13	POLR2A	chr12:50141036-50141693	HepG2	liver:	n/a	n/a
14	POLR2A	chr12:50140958-50141749	K562	blood:	n/a	n/a
15	POLR2A	chr12:50141069-50142595	GM12878	blood:	n/a	n/a
16	POLR2A	chr12:50141021-50141481	K562	blood:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:50141422..50142941-chr12:50168874..50170719,2	K562	blood:
2	chr12:50137626..50141652-chr12:50149897..50153012,3	K562	blood:
3	chr12:50141258..50143607-chr12:50154074..50155843,2	K562	blood:
4	chr12:50038466..50041675-chr12:50139974..50141821,3	K562	blood:
5	chr12:50141439..50143610-chr12:50160538..50162943,2	MCF-7	breast:
6	chr12:50030562..50034220-chr12:50141044..50143029,3	K562	blood:

No data

Variant related genes	Relation type
TMBIM6	TF binding region
ENSG00000139644	Chromatin interaction
ENSG00000110844	Chromatin interaction
ENSG00000161791	Chromatin interaction

Extended variants
information (count: 86 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs1049986	0.82[YRI][hapmap];0.85[AMR][1000 genomes]
rs10875964	0.85[AMR][1000 genomes]
rs10875968	1.00[CEU][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11169080	0.91[CEU][hapmap];0.86[JPT][hapmap];0.92[YRI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11169097	0.85[AMR][1000 genomes]
rs11169101	0.91[CEU][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11169104	0.85[AMR][1000 genomes]
rs11169106	0.82[YRI][hapmap];0.85[AMR][1000 genomes]
rs11169109	0.89[AMR][1000 genomes]
rs11169111	0.85[AMR][1000 genomes]
rs11169112	0.85[AMR][1000 genomes]
rs11169113	0.85[AMR][1000 genomes]
rs11169118	0.89[AMR][1000 genomes]
rs11169125	0.89[AMR][1000 genomes]
rs11169127	0.87[AMR][1000 genomes]
rs11169133	0.89[AMR][1000 genomes]
rs11834380	0.82[YRI][hapmap];0.85[AMR][1000 genomes]
rs12296586	0.89[AMR][1000 genomes]
rs12301824	0.81[AMR][1000 genomes]
rs12303310	0.81[AMR][1000 genomes]
rs12304796	0.85[AMR][1000 genomes]
rs12305460	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12308256	0.85[AMR][1000 genomes]
rs12310510	0.85[AMR][1000 genomes]
rs12314795	0.89[AMR][1000 genomes]
rs12315224	0.89[AMR][1000 genomes]
rs12315732	1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs12315791	0.81[AMR][1000 genomes]
rs12316284	0.82[YRI][hapmap];0.85[AMR][1000 genomes]
rs12317646	0.85[AMR][1000 genomes]
rs12321169	0.89[AMR][1000 genomes]
rs1470906	0.89[AMR][1000 genomes]
rs1574326	0.82[YRI][hapmap];0.89[AMR][1000 genomes]
rs17123981	1.00[CEU][hapmap];0.92[YRI][hapmap];0.81[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs2278068	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs2336058	0.82[YRI][hapmap];0.89[AMR][1000 genomes]
rs28654319	0.84[ASN][1000 genomes]
rs2878532	1.00[CEU][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3887727	0.91[CEU][hapmap];0.86[JPT][hapmap];0.92[YRI][hapmap];0.83[EUR][1000 genomes]
rs4073998	1.00[CEU][hapmap];0.85[JPT][hapmap];0.96[YRI][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4133070	0.82[YRI][hapmap];0.85[AMR][1000 genomes]
rs4563	0.89[AMR][1000 genomes]
rs4584654	0.82[YRI][hapmap];0.89[AMR][1000 genomes]
rs57342147	0.87[AMR][1000 genomes]
rs57463238	0.85[AMR][1000 genomes]
rs58250762	0.84[ASN][1000 genomes]
rs58446833	0.87[AMR][1000 genomes]
rs59233136	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59849800	0.87[AMR][1000 genomes]
rs60402517	0.91[AMR][1000 genomes]
rs61512987	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs61616163	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs61620972	0.85[AMR][1000 genomes]
rs61710637	0.89[AMR][1000 genomes]
rs6580719	0.85[AMR][1000 genomes]
rs7136052	0.89[AMR][1000 genomes]
rs7137976	0.82[YRI][hapmap];0.89[AMR][1000 genomes]
rs7299002	0.85[AMR][1000 genomes]
rs7299609	1.00[CEU][hapmap];0.96[YRI][hapmap];0.85[EUR][1000 genomes]
rs7306877	0.86[EUR][1000 genomes]
rs7309607	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7312658	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7313738	0.89[AMR][1000 genomes]
rs73305085	0.81[AMR][1000 genomes]
rs73305098	0.81[AMR][1000 genomes]
rs73306808	0.85[AMR][1000 genomes]
rs73309030	0.85[AMR][1000 genomes]
rs7688	0.82[YRI][hapmap];0.85[AMR][1000 genomes]
rs7954994	0.85[YRI][hapmap];0.85[AMR][1000 genomes]
rs7955586	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7956089	0.89[AMR][1000 genomes]
rs7956181	0.81[AMR][1000 genomes]
rs7962645	0.89[AMR][1000 genomes]
rs7962863	1.00[CEU][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7963954	0.84[CEU][hapmap];0.86[JPT][hapmap]
rs7965658	0.86[JPT][hapmap]
rs7967624	0.85[AMR][1000 genomes]
rs7979262	0.85[AMR][1000 genomes]
rs7979285	0.91[CEU][hapmap];0.93[YRI][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7980979	0.89[AMR][1000 genomes]
rs8626	1.00[CEU][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs897056	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9804749	0.87[AMR][1000 genomes]
rs9804971	0.89[AMR][1000 genomes]

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	nsv1045327	chr12:49975040-50551375	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases
2	nsv541490	chr12:49975040-50551375	Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:50136600-50146400	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr12:50136800-50144200	Enhancers	Primary T helper naive cells from peripheral blood	blood
3	chr12:50136800-50146600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
4	chr12:50137000-50142000	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr12:50137000-50142200	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr12:50137000-50143800	Weak transcription	Colonic Mucosa	Colon
7	chr12:50137000-50146200	Weak transcription	HSMMtube	muscle
8	chr12:50137000-50147000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr12:50137200-50146200	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr12:50137200-50152000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr12:50137400-50142000	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr12:50137400-50143200	Strong transcription	Fetal Thymus	thymus
13	chr12:50137400-50146400	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr12:50137400-50146400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
15	chr12:50137400-50146600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr12:50137400-50150800	Weak transcription	Fetal Brain Male	brain
17	chr12:50137600-50146200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
18	chr12:50137800-50142000	Weak transcription	HUES48 Cell Line	embryonic stem cell
19	chr12:50137800-50142200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr12:50137800-50142200	Weak transcription	HSMM	muscle
21	chr12:50137800-50143800	Weak transcription	Fetal Stomach	stomach
22	chr12:50137800-50144200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr12:50137800-50146200	Weak transcription	Fetal Kidney	kidney
24	chr12:50138000-50143800	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr12:50138200-50146400	Weak transcription	Fetal Brain Female	brain
26	chr12:50138400-50143000	Weak transcription	Stomach Mucosa	stomach
27	chr12:50138400-50144000	Weak transcription	Fetal Lung	lung
28	chr12:50138600-50141600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr12:50138600-50142000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr12:50138600-50142200	Weak transcription	Brain Anterior Caudate	brain
31	chr12:50138600-50142600	Weak transcription	Pancreatic Islets	Pancreatic Islet
32	chr12:50138600-50142800	Weak transcription	NH-A	brain
33	chr12:50138600-50143400	Weak transcription	Fetal Muscle Trunk	muscle
34	chr12:50138600-50143800	Weak transcription	Primary hematopoietic stem cells	blood
35	chr12:50138600-50143800	Weak transcription	Small Intestine	intestine
36	chr12:50138600-50144000	Weak transcription	Esophagus	oesophagus
37	chr12:50138600-50144200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr12:50138600-50146400	Weak transcription	Brain Germinal Matrix	brain
39	chr12:50138800-50142000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
40	chr12:50138800-50142000	Weak transcription	Osteobl	bone
41	chr12:50138800-50143800	Weak transcription	Rectal Smooth Muscle	rectum
42	chr12:50138800-50143800	Weak transcription	NHLF	lung
43	chr12:50138800-50144000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr12:50139000-50142000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
45	chr12:50139000-50142000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr12:50139000-50142000	Weak transcription	NHDF-Ad	bronchial
47	chr12:50139000-50142200	Enhancers	Fetal Heart	heart
48	chr12:50139000-50142800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
49	chr12:50139000-50143800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
50	chr12:50139000-50143800	Weak transcription	Muscle Satellite Cultured Cells	--

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