Variant report

Variant	rs2270777
Chromosome Location	chr12:58145156-58145157
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	chr12:58144100-58147043	MCF10A-Er-Src	breast:	n/a	n/a
2	E2F4	chr12:58144943-58146556	K562	blood:	n/a	chr12:58145913-58145922 chr12:58146390-58146399 chr12:58145848-58145860
3	TBP	chr12:58145130-58146752	K562	blood:	n/a	n/a
4	POLR2A	chr12:58144509-58146962	K562	blood:	n/a	n/a
5	POLR2A	chr12:58144474-58146332	GM12891	blood:	n/a	n/a
6	POLR2A	chr12:58144955-58146657	HCT-116	colon:	n/a	n/a
7	POLR2A	chr12:58144170-58146625	Hela-S3	cervix:	n/a	n/a
8	STAT5A	chr12:58144840-58145330	GM12878	blood:	n/a	n/a
9	WRNIP1	chr12:58144572-58146586	GM12878	blood:	n/a	n/a
10	POLR2A	chr12:58144208-58146680	GM18505	blood:	n/a	n/a
11	POLR2A	chr12:58144638-58146721	GM18951	blood:	n/a	n/a
12	POLR2A	chr12:58144414-58146731	GM19099	blood:	n/a	n/a
13	POLR2A	chr12:58144700-58146677	K562	blood:	n/a	n/a
14	POLR2A	chr12:58144292-58146326	H1-hESC	embryonic stem cell:	n/a	n/a
15	POLR2A	chr12:58144023-58146704	K562	blood:	n/a	n/a
16	POLR2A	chr12:58144790-58145714	SK-N-SH	brain:	n/a	n/a
17	POLR2A	chr12:58144401-58146211	U87	brain:	n/a	n/a
18	POLR2A	chr12:58144461-58146735	K562	blood:	n/a	n/a
19	POLR2A	chr12:58144987-58146740	Raji	blood:	n/a	n/a
20	JUND	chr12:58144791-58146763	K562	blood:	n/a	chr12:58145912-58145921 chr12:58145680-58145688 chr12:58145680-58145687
21	POLR2A	chr12:58144044-58146752	GM12878	blood:	n/a	n/a
22	POLR2A	chr12:58145095-58146389	H1-hESC	embryonic stem cell:	n/a	n/a
23	YY1	chr12:58145061-58146459	GM12878	blood:	n/a	chr12:58146390-58146401 chr12:58145155-58145177 chr12:58145976-58145990 chr12:58146264-58146273 chr12:58145166-58145174
24	MXI1	chr12:58145015-58146851	IMR90	lung:	n/a	chr12:58146430-58146445 chr12:58146432-58146447 chr12:58146283-58146292
25	ELK1	chr12:58145049-58145265	K562	blood:	n/a	n/a
26	POLR2A	chr12:58144636-58146589	PANC-1	pancreas:	n/a	n/a
27	POLR2A	chr12:58144138-58146600	K562	blood:	n/a	n/a
28	BCLAF1	chr12:58145114-58146248	GM12878	blood:	n/a	n/a
29	POLR2A	chr12:58143986-58146704	MCF-7	breast:	n/a	n/a
30	POLR2A	chr12:58144955-58146948	HUVEC	blood vessel:	n/a	n/a
31	POLR2A	chr12:58143976-58146339	GM12892	blood:	n/a	n/a
32	EP300	chr12:58144390-58147030	SK-N-SH	brain:	n/a	chr12:58145773-58145780 chr12:58146625-58146632 chr12:58145997-58146013 chr12:58146991-58147005
33	USF1	chr12:58145135-58146736	HCT-116	colon:	n/a	chr12:58146356-58146365 chr12:58146188-58146197 chr12:58146119-58146130 chr12:58146187-58146196 chr12:58146355-58146364 chr12:58146185-58146198 chr12:58146187-58146196 chr12:58146186-58146195 chr12:58146380-58146396 chr12:58146353-58146366 chr12:58146355-58146364 chr12:58146354-58146363 chr12:58146181-58146202
34	YY1	chr12:58145039-58145719	K562	blood:	n/a	chr12:58145155-58145177 chr12:58145166-58145174
35	POLR2A	chr12:58144678-58146587	GM12878	blood:	n/a	n/a
36	POLR2A	chr12:58144940-58146703	GM18526	blood:	n/a	n/a
37	POLR2A	chr12:58144145-58147295	HepG2	liver:	n/a	n/a
38	CUX1	chr12:58145101-58145228	K562	blood:	n/a	n/a
39	POLR2A	chr12:58143933-58146798	GM12891	blood:	n/a	n/a
40	JUN	chr12:58144345-58147068	K562	blood:	n/a	chr12:58145912-58145921 chr12:58145680-58145688 chr12:58145680-58145687
41	POLR2A	chr12:58144142-58146803	U87	brain:	n/a	n/a
42	POLR2A	chr12:58144888-58146666	GM15510	blood:	n/a	n/a
43	POLR2A	chr12:58144156-58146867	PBDE	blood:	n/a	n/a
44	CEBPD	chr12:58145142-58146636	K562	blood:	n/a	n/a
45	POLR2A	chr12:58144141-58146736	HepG2	liver:	n/a	n/a
46	SMARCC2	chr12:58145138-58146543	Hela-S3	cervix:	n/a	n/a
47	POLR2A	chr12:58143923-58146757	SK-N-SH	brain:	n/a	n/a
48	POLR2A	chr12:58144450-58146609	GM12878	blood:	n/a	n/a
49	POLR2A	chr12:58144710-58146818	HUVEC	blood vessel:	n/a	n/a
50	POLR2A	chr12:58143934-58145276	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:57940172..57943060-chr12:58144511..58146770,2	K562	blood:
2	chr12:57080844..57082659-chr12:58144695..58147272,2	K562	blood:
3	chr12:57853636..57856322-chr12:58144624..58147677,3	K562	blood:
4	chr12:57914797..57916581-chr12:58144797..58147078,2	MCF-7	breast:
5	chr12:57914860..57917603-chr12:58144909..58148802,3	K562	blood:
6	chr12:57853636..57856322-chr12:58144624..58146178,2	K562	blood:
7	chr12:57480031..57482599-chr12:58144777..58147375,2	MCF-7	breast:
8	chr12:57983953..57986282-chr12:58144732..58146492,2	K562	blood:
9	chr12:57911462..57914270-chr12:58144691..58146581,3	MCF-7	breast:
10	chr12:57851728..57854572-chr12:58144859..58146430,2	MCF-7	breast:
11	chr12:57975136..57977432-chr12:58144177..58146349,2	K562	blood:
12	chr12:57983000..57984965-chr12:58144459..58146652,2	MCF-7	breast:
13	chr12:57999383..58001566-chr12:58144554..58147066,2	K562	blood:
14	chr12:58144944..58148202-chr12:58236897..58241575,4	MCF-7	breast:
15	chr12:57921185..57924132-chr12:58144470..58146639,2	MCF-7	breast:
16	chr12:58144058..58148099-chr12:58238749..58241436,3	K562	blood:
17	chr12:57909291..57914221-chr12:58144639..58148673,6	K562	blood:
18	chr12:57915553..57917499-chr12:58144787..58147876,3	K562	blood:

Variant related genes	Relation type
CDK4	TF binding region
MARCH9	TF binding region
ENSG00000155980	Chromatin interaction
ENSG00000175215	Chromatin interaction
ENSG00000110958	Chromatin interaction
ENSG00000111087	Chromatin interaction
ENSG00000166987	Chromatin interaction
ENSG00000208028	Chromatin interaction
ENSG00000166908	Chromatin interaction
ENSG00000178498	Chromatin interaction
ENSG00000166881	Chromatin interaction
ENSG00000175203	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs1050045	0.96[CEU][hapmap];0.87[TSI][hapmap]
rs10877020	0.82[GIH][hapmap]
rs11172337	0.84[EUR][1000 genomes]
rs12368653	0.84[GIH][hapmap];0.85[JPT][hapmap];0.85[TSI][hapmap];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12371356	0.84[GIH][hapmap];0.83[TSI][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1633359	0.82[AMR][1000 genomes]
rs17852479	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2277326	0.88[CEU][hapmap];0.87[CHD][hapmap];0.97[GIH][hapmap];0.83[TSI][hapmap];0.84[EUR][1000 genomes]
rs2307097	0.88[CEU][hapmap];0.87[CHD][hapmap];0.97[GIH][hapmap];0.83[TSI][hapmap];0.84[EUR][1000 genomes]
rs701007	0.84[AMR][1000 genomes]
rs7295422	0.92[CEU][hapmap];0.86[GIH][hapmap];0.87[TSI][hapmap]
rs7311632	0.88[CEU][hapmap];0.86[GIH][hapmap];0.87[TSI][hapmap]
rs7966795	0.84[CEU][hapmap]
rs799265	0.96[CEU][hapmap];0.87[TSI][hapmap]
rs799267	0.81[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1038741	chr12:57877355-58174506	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
2	nsv541503	chr12:57877355-58174506	Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS 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 miRNA target site	126 gene(s)	inside rSNPs	diseases
3	nsv899121	chr12:58079825-58177292	Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
4	nsv559045	chr12:58112189-58165085	Enhancers Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
5	nsv470296	chr12:58112189-58177292	Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
6	nsv899123	chr12:58118248-58155023	Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
7	nsv826384	chr12:58124758-58157850	Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
8	nsv510601	chr12:58130298-58191925	Flanking Active TSS Bivalent/Poised TSS Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
9	nsv470297	chr12:58133256-58202419	Weak transcription Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
10	nsv826386	chr12:58135303-58150535	Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Weak transcription	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
11	nsv973963	chr12:58138245-58145482	Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2270777	XRCC6BP1	cis	Artery Tibial	GTEx
rs2270777	DKFZP586D0919	cis	multi-tissue	Pritchard
rs2270777	FAM119B	cis	lymphoblastoid	seeQTL
rs2270777	TSFM	Cis_1M	lymphoblastoid	RTeQTL
rs2270777	XRCC6BP1	cis	Muscle Skeletal	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:58139400-58145400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr12:58143200-58145200	Weak transcription	Aorta	Aorta
3	chr12:58143400-58145200	Weak transcription	Primary neutrophils fromperipheralblood	blood
4	chr12:58144000-58145400	Transcr. at gene 5' and 3'	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr12:58144200-58145200	Transcr. at gene 5' and 3'	H9 Cell Line	embryonic stem cell
6	chr12:58144200-58145200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr12:58144200-58145200	Genic enhancers	Spleen	Spleen
8	chr12:58144400-58145200	Transcr. at gene 5' and 3'	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr12:58144400-58145200	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr12:58144400-58145200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
11	chr12:58144400-58145200	Genic enhancers	Gastric	stomach
12	chr12:58144400-58145200	Enhancers	Right Atrium	heart
13	chr12:58144400-58145200	Transcr. at gene 5' and 3'	K562	blood
14	chr12:58144400-58145200	Transcr. at gene 5' and 3'	NHLF	lung
15	chr12:58144400-58145400	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells short term culture	blood
16	chr12:58144400-58145400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr12:58144400-58145400	Transcr. at gene 5' and 3'	A549	lung
18	chr12:58144400-58145400	Transcr. at gene 5' and 3'	Dnd41	blood
19	chr12:58144600-58145200	Transcr. at gene 5' and 3'	HUES6 Cell Line	embryonic stem cell
20	chr12:58144600-58145200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr12:58144600-58145200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
22	chr12:58144600-58145200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
23	chr12:58144600-58145200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr12:58144600-58145200	Enhancers	Ovary	ovary
25	chr12:58144600-58145200	Transcr. at gene 5' and 3'	HSMM	muscle
26	chr12:58144600-58145200	Transcr. at gene 5' and 3'	NHEK	skin
27	chr12:58144600-58145200	Transcr. at gene 5' and 3'	Osteobl	bone
28	chr12:58144600-58145400	Enhancers	Primary B cells from cord blood	blood
29	chr12:58144600-58145400	Transcr. at gene 5' and 3'	Fetal Lung	lung
30	chr12:58144600-58145800	Flanking Active TSS	Fetal Brain Female	brain
31	chr12:58144600-58146000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr12:58144800-58145200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr12:58144800-58145200	Transcr. at gene 5' and 3'	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr12:58144800-58145200	Transcr. at gene 5' and 3'	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr12:58144800-58145200	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
36	chr12:58144800-58145200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
37	chr12:58144800-58145200	Active TSS	Primary T killer memory cells from peripheral blood	blood
38	chr12:58144800-58145200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
39	chr12:58144800-58145200	Transcr. at gene 5' and 3'	Cortex derived primary cultured neurospheres	brain
40	chr12:58144800-58145200	Transcr. at gene 5' and 3'	Fetal Adrenal Gland	Adrenal Gland
41	chr12:58144800-58145200	Transcr. at gene 5' and 3'	Fetal Muscle Leg	muscle
42	chr12:58144800-58145200	Genic enhancers	Placenta	Placenta
43	chr12:58144800-58145200	Enhancers	Lung	lung
44	chr12:58144800-58145200	Enhancers	Placenta Amnion	Placenta Amnion
45	chr12:58144800-58145200	Enhancers	Sigmoid Colon	Sigmoid Colon
46	chr12:58144800-58145200	Enhancers	Stomach Mucosa	stomach
47	chr12:58144800-58145200	Flanking Active TSS	HSMMtube	muscle
48	chr12:58144800-58145400	Flanking Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
49	chr12:58144800-58145400	Enhancers	Primary B cells from peripheral blood	blood
50	chr12:58144800-58145400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain

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