Variant report

Variant	rs2293449
Chromosome Location	chr12:49318546-49318547
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	CTCF	chr12:49318460-49318610	AG04450	lung:	n/a	n/a
2	CTCF	chr12:49318440-49318590	GM12864	blood:	n/a	n/a
3	MAX	chr12:49318443-49319168	H1-hESC	embryonic stem cell:	n/a	chr12:49318695-49318702 chr12:49318745-49318754 chr12:49318693-49318704 chr12:49318693-49318703 chr12:49318694-49318703 chr12:49318690-49318705 chr12:49318693-49318704 chr12:49318743-49318756 chr12:49318694-49318703 chr12:49318744-49318755 chr12:49318692-49318705 chr12:49318694-49318704
4	ELF1	chr12:49318291-49319474	GM12878	blood:	n/a	n/a
5	CTCF	chr12:49318440-49318590	NHDF-neo	bronchial:	n/a	n/a
6	CTCF	chr12:49318392-49318621	GM13976	blood:	n/a	n/a
7	CTCF	chr12:49318420-49318570	HCM	heart:	n/a	n/a
8	CTCF	chr12:49318326-49318619	A549	lung:	n/a	n/a
9	POLR2A	chr12:49318295-49319719	GM12892	blood:	n/a	n/a
10	POLR2A	chr12:49318179-49319816	GM12892	blood:	n/a	n/a
11	RELA	chr12:49318165-49319537	GM19193	blood:	n/a	chr12:49318256-49318265 chr12:49318256-49318265
12	TBL1XR1	chr12:49318368-49318727	GM12878	blood:	n/a	n/a
13	TAF1	chr12:49318428-49318700	H1-hESC	embryonic stem cell:	n/a	n/a
14	RELA	chr12:49318175-49318785	GM18951	blood:	n/a	chr12:49318256-49318265 chr12:49318256-49318265
15	ZBTB7A	chr12:49318276-49319617	ECC-1	luminal epithelium:	n/a	n/a
16	CTCF	chr12:49318400-49318550	GM12870	blood:	n/a	n/a
17	TAF1	chr12:49318407-49319544	H1-hESC	embryonic stem cell:	n/a	n/a
18	CTCF	chr12:49318420-49318570	GM12865	blood:	n/a	n/a
19	CREB1	chr12:49318336-49318877	A549	lung:	n/a	n/a
20	USF2	chr12:49318333-49318868	GM12878	blood:	n/a	n/a
21	CTCF	chr12:49318420-49318570	SK-N-SH_RA	brain:	n/a	n/a
22	CTCF	chr12:49318460-49318610	GM12865	blood:	n/a	n/a
23	RAD21	chr12:49318356-49318721	H1-hESC	embryonic stem cell:	n/a	n/a
24	CTCF	chr12:49318420-49318570	GM12872	blood:	n/a	n/a
25	CTCF	chr12:49318440-49318590	GM12878	blood:	n/a	n/a
26	POLR2A	chr12:49318294-49319845	MCF-7	breast:	n/a	n/a
27	CTCF	chr12:49318440-49318590	Hela-S3	cervix:	n/a	n/a
28	ELF1	chr12:49318299-49318698	A549	lung:	n/a	n/a
29	CTCF	chr12:49318387-49318608	HUVEC	blood vessel:	n/a	n/a
30	CTCF	chr12:49318400-49318550	HepG2	liver:	n/a	n/a
31	CTCF	chr12:49318400-49318550	HL-60	blood:	n/a	n/a
32	CTCF	chr12:49318420-49318570	GM12874	blood:	n/a	n/a
33	ATF2	chr12:49318198-49318892	GM12878	blood:	n/a	chr12:49318762-49318776
34	CTCF	chr12:49318420-49318570	HRE	kidney:	n/a	n/a
35	RAD21	chr12:49318337-49318649	SK-N-SH_RA	brain:	n/a	n/a
36	CTCF	chr12:49318296-49318732	GM12878	blood:	n/a	n/a
37	CTCF	chr12:49318440-49318590	GM12874	blood:	n/a	n/a
38	MAX	chr12:49318314-49319133	ECC-1	luminal epithelium:	n/a	chr12:49318695-49318702 chr12:49318745-49318754 chr12:49318693-49318704 chr12:49318693-49318703 chr12:49318694-49318703 chr12:49318690-49318705 chr12:49318693-49318704 chr12:49318743-49318756 chr12:49318694-49318703 chr12:49318744-49318755 chr12:49318692-49318705 chr12:49318694-49318704
39	MAX	chr12:49318264-49319714	A549	lung:	n/a	chr12:49318695-49318702 chr12:49318745-49318754 chr12:49318693-49318704 chr12:49318693-49318703 chr12:49318694-49318703 chr12:49318690-49318705 chr12:49318693-49318704 chr12:49318743-49318756 chr12:49318694-49318703 chr12:49318744-49318755 chr12:49318692-49318705 chr12:49318694-49318704
40	CTCF	chr12:49318333-49318702	IMR90	lung:	n/a	n/a
41	CTCF	chr12:49318400-49318550	AG10803	skin:	n/a	n/a
42	ZNF143	chr12:49318330-49318699	GM12878	blood:	n/a	chr12:49318469-49318487
43	MXI1	chr12:49318488-49318740	HepG2	liver:	n/a	n/a
44	CTCF	chr12:49318400-49318550	A549	lung:	n/a	n/a
45	CHD2	chr12:49318506-49318687	H1-hESC	embryonic stem cell:	n/a	n/a
46	STAT5A	chr12:49318171-49318723	GM12878	blood:	n/a	n/a
47	CTCF	chr12:49318480-49318630	NHLF	lung:	n/a	n/a
48	CTCF	chr12:49318420-49318570	GM12870	blood:	n/a	n/a
49	CTCF	chr12:49318460-49318610	HMF	breast:	n/a	n/a
50	POLR2A	chr12:49318491-49319551	GM10847	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:49212473..49213308-chr12:49318055..49318794,2	MCF-7	breast:
2	chr12:49211386..49213758-chr12:49317822..49319346,2	MCF-7	breast:
3	chr12:49316917..49319846-chr12:49321799..49325494,4	K562	blood:
4	chr12:49317412..49320697-chr12:49349793..49352537,4	MCF-7	breast:
5	chr12:49318409..49320473-chr12:49386787..49389154,2	MCF-7	breast:
6	chr12:49257454..49260772-chr12:49317154..49320539,3	MCF-7	breast:
7	chr12:49245963..49247751-chr12:49317835..49320703,2	MCF-7	breast:
8	chr12:49258143..49260662-chr12:49316104..49319150,3	MCF-7	breast:

Variant related genes	Relation type
FKBP11	TF binding region
ENSG00000258283	Chromatin interaction
ENSG00000272822	Chromatin interaction
ENSG00000134287	Chromatin interaction
ENSG00000174243	Chromatin interaction
ENSG00000172602	Chromatin interaction
ENSG00000167535	Chromatin interaction
ENSG00000201678	Chromatin interaction

Extended variants
information (count: 130 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:127)

rs_ID	r²[population]
rs1051886	1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs1054376	1.00[CHB][hapmap];0.88[JPT][hapmap];0.92[ASN][1000 genomes]
rs10747556	0.96[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs10747557	1.00[CHB][hapmap];0.81[JPT][hapmap];0.92[ASN][1000 genomes]
rs10747558	0.95[CHB][hapmap];0.92[ASN][1000 genomes]
rs10783287	0.81[CEU][hapmap]
rs10783289	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs10783290	0.90[ASN][1000 genomes]
rs10783292	0.92[ASN][1000 genomes]
rs10783293	1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs10783294	1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs10783295	0.97[ASN][1000 genomes]
rs10783297	0.92[ASN][1000 genomes]
rs10875883	0.83[CHB][hapmap]
rs10875885	0.83[CHB][hapmap]
rs10875886	1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs10875888	0.86[ASN][1000 genomes]
rs10875893	1.00[CHB][hapmap];0.90[JPT][hapmap];0.94[ASN][1000 genomes]
rs10875894	1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs10875895	0.97[ASN][1000 genomes]
rs10875896	0.92[ASN][1000 genomes]
rs10875897	0.95[CHB][hapmap];0.90[JPT][hapmap];0.92[ASN][1000 genomes]
rs10875898	0.95[CHB][hapmap];0.85[JPT][hapmap];0.92[ASN][1000 genomes]
rs10875899	0.81[ASN][1000 genomes]
rs10875900	0.92[ASN][1000 genomes]
rs10875901	0.91[ASN][1000 genomes]
rs10875902	0.95[CHB][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs1111662	1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs11168779	0.94[ASN][1000 genomes]
rs11168783	1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs11168784	1.00[CHB][hapmap];0.91[JPT][hapmap];0.95[ASN][1000 genomes]
rs11168785	1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs11168790	1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs11168792	0.97[ASN][1000 genomes]
rs11168794	0.97[ASN][1000 genomes]
rs11168795	0.92[ASN][1000 genomes]
rs11168797	0.93[ASN][1000 genomes]
rs11168798	0.86[ASN][1000 genomes]
rs11168800	0.86[ASN][1000 genomes]
rs11168801	0.86[ASN][1000 genomes]
rs11168803	0.92[ASN][1000 genomes]
rs11168811	0.83[ASN][1000 genomes]
rs11168812	0.91[ASN][1000 genomes]
rs11608916	0.96[ASN][1000 genomes]
rs11610459	0.97[ASN][1000 genomes]
rs11610497	0.97[ASN][1000 genomes]
rs11614474	0.97[ASN][1000 genomes]
rs12227240	0.92[ASN][1000 genomes]
rs12228521	0.94[ASN][1000 genomes]
rs12229275	0.95[ASN][1000 genomes]
rs12369505	0.80[CHB][hapmap]
rs12423542	1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs12579249	0.97[ASN][1000 genomes]
rs1318692	0.95[ASN][1000 genomes]
rs1690182	0.90[ASN][1000 genomes]
rs1818996	0.92[ASN][1000 genomes]
rs1830192	0.96[CHB][hapmap];0.86[JPT][hapmap];0.92[ASN][1000 genomes]
rs2030900	0.95[CHB][hapmap];0.86[JPT][hapmap];0.93[ASN][1000 genomes]
rs2070940	0.96[CHB][hapmap];0.86[JPT][hapmap];0.90[ASN][1000 genomes]
rs2073480	1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs2131713	0.95[CHB][hapmap];0.89[JPT][hapmap];0.92[ASN][1000 genomes]
rs2272311	0.95[CHB][hapmap];0.90[JPT][hapmap];0.92[ASN][1000 genomes]
rs2272312	1.00[CHB][hapmap];0.90[JPT][hapmap];0.98[ASN][1000 genomes]
rs2368701	0.94[ASN][1000 genomes]
rs2446999	0.80[CEU][hapmap]
rs2453063	0.92[ASN][1000 genomes]
rs2463175	0.90[ASN][1000 genomes]
rs2641450	0.88[ASN][1000 genomes]
rs2694839	0.90[ASN][1000 genomes]
rs2694840	0.89[ASN][1000 genomes]
rs2926806	0.80[CEU][hapmap]
rs2934998	0.80[CEU][hapmap]
rs3741627	1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs3759146	1.00[CHB][hapmap];0.95[JPT][hapmap];0.98[ASN][1000 genomes]
rs3782353	1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs3809147	1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs3825182	1.00[CHB][hapmap];0.95[JPT][hapmap];0.98[ASN][1000 genomes]
rs3825184	1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs4018510	0.92[ASN][1000 genomes]
rs4237854	1.00[CHB][hapmap];0.91[JPT][hapmap];0.97[ASN][1000 genomes]
rs4433614	1.00[CHB][hapmap];0.91[JPT][hapmap];0.95[ASN][1000 genomes]
rs4526804	0.91[ASN][1000 genomes]
rs4760600	1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs4760661	0.96[ASN][1000 genomes]
rs4760663	0.82[CHB][hapmap];0.81[ASN][1000 genomes]
rs4760664	0.91[ASN][1000 genomes]
rs4760665	0.94[ASN][1000 genomes]
rs4760666	0.91[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs4760667	0.95[CHB][hapmap];0.83[JPT][hapmap];0.92[ASN][1000 genomes]
rs4760668	0.92[ASN][1000 genomes]
rs58023472	0.97[ASN][1000 genomes]
rs59087236	0.91[ASN][1000 genomes]
rs61941142	0.94[ASN][1000 genomes]
rs61942166	0.91[ASN][1000 genomes]
rs61942167	0.93[ASN][1000 genomes]
rs61942169	0.92[ASN][1000 genomes]
rs61942207	0.91[ASN][1000 genomes]
rs61942209	0.85[ASN][1000 genomes]
rs6580696	1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs7134686	0.80[ASN][1000 genomes]
rs7297958	1.00[CHB][hapmap];0.90[JPT][hapmap];0.97[ASN][1000 genomes]
rs7298330	0.97[ASN][1000 genomes]
rs7304942	0.97[ASN][1000 genomes]
rs7313988	0.91[ASN][1000 genomes]
rs7489036	0.91[ASN][1000 genomes]
rs7963018	0.92[ASN][1000 genomes]
rs7963160	0.90[ASN][1000 genomes]
rs7976473	0.89[ASN][1000 genomes]
rs833483	0.80[CEU][hapmap]
rs833484	0.82[CEU][hapmap]
rs833820	0.95[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs833821	0.93[ASN][1000 genomes]
rs833822	0.95[CHB][hapmap];0.90[JPT][hapmap];0.91[ASN][1000 genomes]
rs833827	0.91[ASN][1000 genomes]
rs833828	0.89[ASN][1000 genomes]
rs833839	0.82[CEU][hapmap];0.86[ASN][1000 genomes]
rs833840	0.86[CHB][hapmap];0.86[ASN][1000 genomes]
rs833841	0.81[CEU][hapmap];0.86[CHB][hapmap];0.85[ASN][1000 genomes]
rs833842	0.85[ASN][1000 genomes]
rs833843	0.86[CHB][hapmap];0.82[ASN][1000 genomes]
rs961320	0.95[ASN][1000 genomes]
rs9645813	0.85[ASN][1000 genomes]
rs9783452	0.95[CHB][hapmap];0.90[JPT][hapmap];0.91[ASN][1000 genomes]
rs9783477	0.91[ASN][1000 genomes]
rs9788029	0.99[ASN][1000 genomes]
rs9795742	0.94[ASN][1000 genomes]
rs9796008	0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2293449	CCDC65	cis	Skin Sun Exposed Lower leg	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:49311000-49318600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr12:49313400-49319000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr12:49314400-49318600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr12:49314400-49338000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr12:49314400-49338600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr12:49315800-49321000	Weak transcription	K562	blood
7	chr12:49317200-49319400	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
8	chr12:49317600-49318600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
9	chr12:49317800-49318600	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr12:49317800-49318600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr12:49317800-49318600	Flanking Active TSS	Duodenum Mucosa	Duodenum
12	chr12:49317800-49319400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr12:49317800-49319400	Active TSS	Rectal Mucosa Donor 31	rectum
14	chr12:49318000-49318600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr12:49318000-49318600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr12:49318000-49318600	Flanking Active TSS	Dnd41	blood
17	chr12:49318000-49318600	Transcr. at gene 5' and 3'	HSMM	muscle
18	chr12:49318000-49318800	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
19	chr12:49318000-49319400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr12:49318000-49319400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr12:49318000-49319400	Active TSS	Rectal Smooth Muscle	rectum
22	chr12:49318000-49319800	Active TSS	Pancreatic Islets	Pancreatic Islet
23	chr12:49318200-49318600	Flanking Active TSS	H1 Cell Line	embryonic stem cell
24	chr12:49318200-49318600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr12:49318200-49318600	Transcr. at gene 5' and 3'	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr12:49318200-49318600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr12:49318200-49318600	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
28	chr12:49318200-49318600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
29	chr12:49318200-49318600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
30	chr12:49318200-49318600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
31	chr12:49318200-49318600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr12:49318200-49318600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr12:49318200-49318600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr12:49318200-49318600	Flanking Active TSS	Adipose Nuclei	Adipose
35	chr12:49318200-49318600	Flanking Active TSS	Liver	Liver
36	chr12:49318200-49318600	Flanking Active TSS	Brain Anterior Caudate	brain
37	chr12:49318200-49318600	Flanking Active TSS	Brain Cingulate Gyrus	brain
38	chr12:49318200-49318600	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
39	chr12:49318200-49318600	Flanking Active TSS	Colonic Mucosa	Colon
40	chr12:49318200-49318600	Enhancers	Fetal Brain Male	brain
41	chr12:49318200-49318600	Flanking Active TSS	Fetal Muscle Trunk	muscle
42	chr12:49318200-49318600	Flanking Active TSS	Fetal Muscle Leg	muscle
43	chr12:49318200-49318600	Flanking Active TSS	Fetal Stomach	stomach
44	chr12:49318200-49318600	Flanking Active TSS	Stomach Smooth Muscle	stomach
45	chr12:49318200-49318600	Flanking Active TSS	HMEC	breast
46	chr12:49318200-49318600	Flanking Active TSS	HUVEC	blood vessel
47	chr12:49318200-49318600	Flanking Active TSS	NHEK	skin
48	chr12:49318200-49318800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
49	chr12:49318200-49318800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr12:49318200-49318800	Flanking Active TSS	Brain Hippocampus Middle	brain

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