Variant report

Variant	rs17034931
Chromosome Location	chr12:104325459-104325460
allele	C/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	RCOR1	chr12:104323737-104325674	GM12878	blood:	n/a	n/a
2	POLR2A	chr12:104325096-104325540	U87	brain:	n/a	n/a
3	RUNX3	chr12:104321971-104325533	GM12878	blood:	n/a	n/a
4	POLR2A	chr12:104322428-104325591	SK-N-MC	brain:	n/a	n/a
5	WRNIP1	chr12:104322092-104325599	GM12878	blood:	n/a	n/a
6	MAX	chr12:104322651-104325593	A549	lung:	n/a	chr12:104324136-104324146 chr12:104324993-104325000 chr12:104324419-104324429 chr12:104323780-104323789 chr12:104324642-104324652 chr12:104323784-104323793 chr12:104323936-104323951 chr12:104324369-104324379
7	POLR2A	chr12:104323967-104325720	GM12891	blood:	n/a	n/a
8	TEAD4	chr12:104322407-104327510	K562	blood:	n/a	n/a
9	POLR2A	chr12:104323006-104326144	IMR90	lung:	n/a	n/a
10	MTA3	chr12:104321890-104325504	GM12878	blood:	n/a	n/a
11	RFX5	chr12:104322611-104325806	SK-N-SH	brain:	n/a	chr12:104323780-104323789 chr12:104323777-104323791 chr12:104323779-104323794 chr12:104323779-104323794 chr12:104323779-104323794 chr12:104323778-104323795
12	POLR2A	chr12:104324627-104325462	HepG2	liver:	n/a	n/a
13	POLR2A	chr12:104324024-104325565	K562	blood:	n/a	n/a
14	POLR2A	chr12:104323979-104325538	PFSK-1	brain:	n/a	n/a
15	POLR2A	chr12:104322849-104325508	Hela-S3	cervix:	n/a	n/a
16	POLR2A	chr12:104323989-104328526	K562	blood:	n/a	n/a
17	POLR2A	chr12:104323632-104325579	GM12892	blood:	n/a	n/a
18	POLR2A	chr12:104322439-104326717	MCF10A-Er-Src	breast:	n/a	n/a
19	POLR2A	chr12:104323645-104325618	H1-hESC	embryonic stem cell:	n/a	n/a
20	PML	chr12:104323762-104328552	K562	blood:	n/a	n/a
21	POLR2A	chr12:104322548-104325574	PBDE	blood:	n/a	n/a
22	POLR2A	chr12:104323674-104325727	PANC-1	pancreas:	n/a	n/a
23	POLR2A	chr12:104321755-104325879	GM12878	blood:	n/a	n/a
24	TBL1XR1	chr12:104323206-104325740	K562	blood:	n/a	n/a
25	POLR2A	chr12:104323921-104325676	K562	blood:	n/a	n/a
26	BCLAF1	chr12:104323952-104325573	GM12878	blood:	n/a	chr12:104324626-104324634 chr12:104324880-104324889
27	POLR2A	chr12:104321980-104325463	GM18526	blood:	n/a	n/a
28	POLR2A	chr12:104320257-104326275	GM12878	blood:	n/a	n/a
29	TBL1XR1	chr12:104325255-104325901	K562	blood:	n/a	n/a
30	POLR2A	chr12:104322749-104325574	HepG2	liver:	n/a	n/a
31	POLR2A	chr12:104321807-104325757	GM12892	blood:	n/a	n/a
32	HEY1	chr12:104324015-104325673	K562	blood:	n/a	chr12:104324191-104324206
33	POLR2A	chr12:104321980-104325932	GM19099	blood:	n/a	n/a
34	POLR2A	chr12:104322047-104327304	GM12878	blood:	n/a	n/a
35	POLR2A	chr12:104321848-104325604	GM12892	blood:	n/a	n/a
36	POLR2A	chr12:104322411-104328493	H1-hESC	embryonic stem cell:	n/a	n/a
37	POLR2A	chr12:104323629-104325550	GM12891	blood:	n/a	n/a
38	POLR2A	chr12:104325358-104325780	HCT-116	colon:	n/a	n/a
39	TBL1XR1	chr12:104322054-104325554	GM12878	blood:	n/a	n/a
40	POLR2A	chr12:104321935-104326151	GM12891	blood:	n/a	n/a
41	CHD2	chr12:104325168-104325474	K562	blood:	n/a	n/a
42	MXI1	chr12:104322168-104325493	GM12878	blood:	n/a	chr12:104323780-104323795 chr12:104323778-104323793
43	POLR2A	chr12:104322001-104325691	GM18505	blood:	n/a	n/a
44	POLR2A	chr12:104322370-104325574	GM12891	blood:	n/a	n/a
45	POLR2A	chr12:104321998-104325551	GM18951	blood:	n/a	n/a
46	POLR2A	chr12:104322713-104325569	H1-hESC	embryonic stem cell:	n/a	n/a
47	POLR2A	chr12:104323697-104325648	HepG2	liver:	n/a	n/a
48	HEY1	chr12:104323958-104325546	K562	blood:	n/a	chr12:104324191-104324206
49	POLR2A	chr12:104322617-104325541	K562	blood:	n/a	n/a
50	POLR2A	chr12:104323743-104328568	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:104320418..104331406-chr12:104346801..104355501,25	MCF-7	breast:
2	chr12:104233909..104239694-chr12:104322835..104327398,8	K562	blood:
3	chr12:104319631..104321504-chr12:104324248..104326474,2	MCF-7	breast:
4	chr12:104319225..104328292-chr12:104356282..104362179,14	K562	blood:
5	chr12:104322684..104325586-chr12:104530441..104532019,2	K562	blood:
6	chr12:104276117..104279238-chr12:104322705..104326968,4	K562	blood:
7	chr1:46152208..46153875-chr12:104323647..104326577,2	K562	blood:
8	chr12:104323659..104328405-chr12:104357607..104360751,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000214198	TF binding region
ENSG00000204954	Chromatin interaction
ENSG00000139372	Chromatin interaction
ENSG00000214198	Chromatin interaction
ENSG00000159596	Chromatin interaction
ENSG00000120837	Chromatin interaction
ENSG00000111696	Chromatin interaction
ENSG00000159592	Chromatin interaction
ENSG00000257327	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10861144	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10861145	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11111812	1.00[CEU][hapmap]
rs11111814	0.94[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.92[JPT][hapmap]
rs11111819	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap]
rs11111820	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs11111825	1.00[CHB][hapmap];0.92[JPT][hapmap];0.81[ASN][1000 genomes]
rs11111829	0.81[ASN][1000 genomes]
rs11111833	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11111835	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[JPT][hapmap];1.00[ASN][1000 genomes]
rs11111837	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11111838	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11111839	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11111842	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11111843	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11111844	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11111846	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11111849	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11111850	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11830285	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.81[ASN][1000 genomes]
rs11831836	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11833702	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12228360	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs17034916	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2576974	0.94[CHB][hapmap];1.00[CHD][hapmap];0.92[JPT][hapmap]
rs2583273	0.93[ASN][1000 genomes]
rs3751206	1.00[CEU][hapmap]
rs3794246	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4135036	1.00[CEU][hapmap]
rs57083451	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58929830	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58943141	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7295489	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7315947	0.81[ASN][1000 genomes]
rs73177915	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73177916	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73177918	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73177919	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73177921	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv560039	chr12:104177668-104455340	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17034931	TU12B1-TY	cis	multi-tissue	Pritchard

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:104322200-104326200	Active TSS	H1 Cell Line	embryonic stem cell
2	chr12:104322200-104326200	Active TSS	GM12878-XiMat	blood
3	chr12:104322400-104325600	Active TSS	H9 Cell Line	embryonic stem cell
4	chr12:104322400-104325800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
5	chr12:104322400-104326000	Active TSS	Colonic Mucosa	Colon
6	chr12:104322400-104326000	Active TSS	Fetal Intestine Small	intestine
7	chr12:104322400-104327000	Active TSS	Right Atrium	heart
8	chr12:104322600-104325600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr12:104322600-104325600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr12:104322600-104325600	Active TSS	Esophagus	oesophagus
11	chr12:104322600-104325600	Active TSS	Sigmoid Colon	Sigmoid Colon
12	chr12:104322600-104325800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr12:104322600-104325800	Active TSS	Fetal Muscle Trunk	muscle
14	chr12:104322600-104326400	Active TSS	iPS-15b Cell Line	embryonic stem cell
15	chr12:104322600-104327000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr12:104322600-104327200	Active TSS	Aorta	Aorta
17	chr12:104322800-104325600	Active TSS	Left Ventricle	heart
18	chr12:104322800-104325600	Active TSS	Lung	lung
19	chr12:104322800-104325600	Active TSS	Small Intestine	intestine
20	chr12:104322800-104326000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
21	chr12:104322800-104326000	Active TSS	Fetal Intestine Large	intestine
22	chr12:104322800-104326000	Active TSS	NHDF-Ad	bronchial
23	chr12:104322800-104326200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr12:104322800-104326200	Active TSS	Fetal Stomach	stomach
25	chr12:104322800-104326200	Active TSS	Ovary	ovary
26	chr12:104322800-104326600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr12:104322800-104326800	Active TSS	Right Ventricle	heart
28	chr12:104323000-104325600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr12:104323000-104325800	Active TSS	Colon Smooth Muscle	Colon
30	chr12:104323000-104326000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
31	chr12:104323000-104326000	Active TSS	Fetal Muscle Leg	muscle
32	chr12:104323000-104326200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr12:104323000-104326200	Active TSS	Psoas Muscle	Psoas
34	chr12:104323200-104325600	Active TSS	Duodenum Smooth Muscle	Duodenum
35	chr12:104323200-104325600	Active TSS	Placenta	Placenta
36	chr12:104323200-104325600	Active TSS	Pancreas	Pancrea
37	chr12:104323200-104325800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr12:104323200-104326400	Active TSS	HSMMtube	muscle
39	chr12:104323400-104325600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr12:104323600-104325800	Active TSS	Fetal Thymus	thymus
41	chr12:104324200-104325600	Flanking Active TSS	Primary hematopoietic stem cells	blood
42	chr12:104324200-104325800	Flanking Active TSS	Primary B cells from cord blood	blood
43	chr12:104324200-104325800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
44	chr12:104324400-104325600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr12:104324600-104325600	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
46	chr12:104324600-104325600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
47	chr12:104324600-104325800	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
48	chr12:104324600-104326000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
49	chr12:104324600-104326200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr12:104324600-104326200	Flanking Active TSS	Adipose Nuclei	Adipose

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