Variant report

Variant	rs12306443
Chromosome Location	chr12:105379674-105379675
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	chr12:105379667-105380496	HUVEC	blood vessel:	n/a	n/a
2	SRF	chr12:105379624-105380380	ECC-1	luminal epithelium:	n/a	n/a
3	POLR2A	chr12:105379579-105380668	SK-N-MC	brain:	n/a	n/a
4	MXI1	chr12:105379588-105380695	GM12878	blood:	n/a	n/a
5	REST	chr12:105379561-105380674	H1-neurons	neurons:	n/a	chr12:105380062-105380075 chr12:105380361-105380374 chr12:105380364-105380377 chr12:105379994-105380007
6	MAX	chr12:105379671-105380699	A549	lung:	n/a	n/a
7	PML	chr12:105379650-105380707	GM12878	blood:	n/a	n/a
8	REST	chr12:105379626-105380452	A549	lung:	n/a	chr12:105380062-105380075 chr12:105380361-105380374 chr12:105380364-105380377 chr12:105379994-105380007
9	POLR2A	chr12:105379663-105380554	K562	blood:	n/a	n/a
10	POLR2A	chr12:105379626-105380437	PFSK-1	brain:	n/a	n/a
11	POLR2A	chr12:105379494-105380737	Raji	blood:	n/a	n/a
12	POLR2A	chr12:105379616-105380941	H1-hESC	embryonic stem cell:	n/a	n/a
13	POLR2A	chr12:105379660-105380333	PANC-1	pancreas:	n/a	n/a
14	MYC	chr12:105379477-105380609	A549	lung:	n/a	n/a
15	MTA3	chr12:105379652-105380386	GM12878	blood:	n/a	n/a
16	POLR2A	chr12:105379543-105380823	GM12891	blood:	n/a	n/a
17	HCFC1	chr12:105379569-105380975	Hela-S3	cervix:	n/a	n/a
18	MXI1	chr12:105379587-105381232	SK-N-SH	brain:	n/a	n/a
19	POLR2A	chr12:105379248-105380699	HepG2	liver:	n/a	n/a
20	NRF1	chr12:105379632-105380316	SK-N-SH	brain:	n/a	chr12:105380067-105380076 chr12:105379976-105379987
21	BCL3	chr12:105379658-105380446	A549	lung:	n/a	chr12:105380396-105380409 chr12:105380430-105380443 chr12:105380296-105380309 chr12:105380433-105380446 chr12:105380368-105380381
22	TCF12	chr12:105379565-105380511	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:105349646..105353787-chr12:105376379..105382982,10	MCF-7	breast:
2	chr12:105379411..105381004-chr12:105501090..105502694,2	MCF-7	breast:
3	chr12:105351138..105353772-chr12:105378582..105380234,3	MCF-7	breast:

Variant related genes	Relation type
C12orf45	TF binding region
ENSG00000136052	Chromatin interaction
ENSG00000136051	Chromatin interaction

Extended variants
information (count: 77 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs10160991	0.84[ASN][1000 genomes]
rs10161522	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10507186	1.00[CEU][hapmap];1.00[GIH][hapmap];0.91[EUR][1000 genomes]
rs10507187	1.00[CEU][hapmap];1.00[GIH][hapmap];0.91[EUR][1000 genomes]
rs10507188	1.00[CEU][hapmap];1.00[GIH][hapmap];0.88[EUR][1000 genomes]
rs11112218	1.00[CEU][hapmap]
rs11112276	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11112277	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11112279	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11112283	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11112303	0.91[EUR][1000 genomes]
rs11112307	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11112346	1.00[CHB][hapmap];0.91[CHD][hapmap];0.81[GIH][hapmap];0.93[JPT][hapmap];0.84[YRI][hapmap]
rs11503466	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12296144	0.97[EUR][1000 genomes]
rs12299385	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12299936	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12300005	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12300010	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12301432	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12301850	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.82[MEX][hapmap];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12306191	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12306848	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12308952	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12310790	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12313077	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12314995	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12315975	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12315983	1.00[CEU][hapmap];0.84[CHB][hapmap];0.81[JPT][hapmap];0.89[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12316001	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12319632	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12320024	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];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12320195	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12320880	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12321224	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12321226	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12321381	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.87[TSI][hapmap];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17036439	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs17036463	1.00[CEU][hapmap];1.00[GIH][hapmap];0.91[EUR][1000 genomes]
rs17036494	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs17036505	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs17036509	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs17036534	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs17036542	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs17036549	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs17036558	0.91[EUR][1000 genomes]
rs17041531	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs35879768	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3812795	1.00[CEU][hapmap];1.00[GIH][hapmap];0.91[EUR][1000 genomes]
rs3935722	0.94[EUR][1000 genomes]
rs4077312	1.00[CEU][hapmap];1.00[GIH][hapmap];0.91[EUR][1000 genomes]
rs4267155	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4268581	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4357778	0.94[EUR][1000 genomes]
rs4375513	1.00[CEU][hapmap]
rs4393405	0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4451800	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4553438	1.00[CEU][hapmap]
rs58005679	0.94[EUR][1000 genomes]
rs58447363	0.94[EUR][1000 genomes]
rs58483223	0.91[EUR][1000 genomes]
rs60057011	0.85[EUR][1000 genomes]
rs60096703	0.91[EUR][1000 genomes]
rs60310033	0.85[EUR][1000 genomes]
rs60809012	0.85[EUR][1000 genomes]
rs60956548	0.94[EUR][1000 genomes]
rs61638859	0.91[EUR][1000 genomes]
rs7131977	1.00[CEU][hapmap];0.90[GIH][hapmap];0.88[TSI][hapmap];0.91[EUR][1000 genomes]
rs7299019	1.00[CEU][hapmap];0.90[GIH][hapmap]
rs73387265	0.91[EUR][1000 genomes]
rs7964906	0.99[ASN][1000 genomes]
rs7970504	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs9738733	0.91[EUR][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	nsv899495	chr12:104990469-105527011	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv899498	chr12:105173598-105461620	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	22 gene(s)	inside rSNPs	diseases
3	nsv832505	chr12:105315352-105497765	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
4	nsv869	chr12:105363425-105394904	Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:105379200-105380600	Active TSS	Liver	Liver
2	chr12:105379200-105380600	Active TSS	Hela-S3	cervix
3	chr12:105379200-105380600	Bivalent/Poised TSS	HepG2	liver
4	chr12:105379200-105380800	Active TSS	Breast Myoepithelial Primary Cells	Breast
5	chr12:105379200-105380800	Active TSS	NHEK	skin
6	chr12:105379200-105381200	Active TSS	Rectal Mucosa Donor 29	rectum
7	chr12:105379200-105381400	Active TSS	Duodenum Mucosa	Duodenum
8	chr12:105379200-105381400	Active TSS	GM12878-XiMat	blood
9	chr12:105379400-105379800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr12:105379400-105379800	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
11	chr12:105379400-105379800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr12:105379400-105379800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
13	chr12:105379400-105379800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
14	chr12:105379400-105379800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
15	chr12:105379400-105379800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
16	chr12:105379400-105379800	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr12:105379400-105379800	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
18	chr12:105379400-105379800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr12:105379400-105379800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr12:105379400-105379800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr12:105379400-105379800	Flanking Active TSS	Brain Anterior Caudate	brain
22	chr12:105379400-105379800	Flanking Active TSS	Brain Substantia Nigra	brain
23	chr12:105379400-105379800	Flanking Active TSS	Placenta	Placenta
24	chr12:105379400-105379800	Enhancers	Pancreas	Pancrea
25	chr12:105379400-105379800	Enhancers	Psoas Muscle	Psoas
26	chr12:105379400-105379800	Enhancers	Spleen	Spleen
27	chr12:105379400-105379800	Flanking Active TSS	A549	lung
28	chr12:105379400-105379800	Flanking Active TSS	Osteobl	bone
29	chr12:105379400-105380000	Flanking Active TSS	Primary B cells from peripheral blood	blood
30	chr12:105379400-105380000	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
31	chr12:105379400-105380000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
32	chr12:105379400-105380000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
33	chr12:105379400-105380000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr12:105379400-105380000	Flanking Active TSS	Dnd41	blood
35	chr12:105379400-105380200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr12:105379400-105380600	Active TSS	Brain Angular Gyrus	brain
37	chr12:105379400-105380600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
38	chr12:105379400-105380600	Active TSS	Duodenum Smooth Muscle	Duodenum
39	chr12:105379400-105380600	Active TSS	Rectal Mucosa Donor 31	rectum
40	chr12:105379400-105380600	Active TSS	Stomach Smooth Muscle	stomach
41	chr12:105379400-105380800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr12:105379400-105380800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr12:105379400-105380800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
44	chr12:105379400-105380800	Active TSS	Brain Cingulate Gyrus	brain
45	chr12:105379400-105381000	Active TSS	Brain Inferior Temporal Lobe	brain
46	chr12:105379400-105381000	Active TSS	Rectal Smooth Muscle	rectum
47	chr12:105379400-105381200	Flanking Active TSS	Primary B cells from cord blood	blood
48	chr12:105379400-105381200	Active TSS	Pancreatic Islets	Pancreatic Islet
49	chr12:105379400-105381600	Active TSS	Colonic Mucosa	Colon
50	chr12:105379600-105379800	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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