Variant report

Variant	rs996513
Chromosome Location	chr2:114649096-114649097
allele	A/C
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	chr2:114648793-114649128	U87	brain:	n/a	n/a
2	STAT3	chr2:114648894-114649291	MCF10A-Er-Src	breast:	n/a	chr2:114649127-114649138 chr2:114649129-114649137
3	IRF1	chr2:114648308-114650459	K562	blood:	n/a	chr2:114649730-114649744 chr2:114650045-114650059
4	NFATC1	chr2:114648225-114649198	GM12878	blood:	n/a	n/a
5	POLR2A	chr2:114643857-114649205	GM12891	blood:	n/a	n/a
6	BCLAF1	chr2:114646904-114649154	GM12878	blood:	n/a	chr2:114648180-114648193 chr2:114648094-114648103 chr2:114647523-114647536 chr2:114648262-114648271
7	POLR2A	chr2:114643825-114649166	GM12892	blood:	n/a	n/a
8	TBP	chr2:114646842-114649197	K562	blood:	n/a	n/a
9	EP300	chr2:114648171-114649246	K562	blood:	n/a	chr2:114649141-114649155
10	POLR2A	chr2:114643910-114650805	GM12878	blood:	n/a	n/a
11	TBP	chr2:114648281-114649217	Hela-S3	cervix:	n/a	n/a
12	CHD2	chr2:114648070-114649105	K562	blood:	n/a	n/a
13	TBP	chr2:114648263-114649183	GM12878	blood:	n/a	n/a
14	JUND	chr2:114646941-114649195	K562	blood:	n/a	chr2:114647000-114647009 chr2:114647383-114647397
15	MXI1	chr2:114646608-114649272	IMR90	lung:	n/a	n/a
16	FOS	chr2:114648947-114649193	MCF10A-Er-Src	breast:	n/a	n/a
17	ZNF384	chr2:114648188-114649905	K562	blood:	n/a	n/a
18	CHD1	chr2:114646374-114649786	GM12878	blood:	n/a	n/a
19	BHLHE40	chr2:114647090-114649118	GM12878	blood:	n/a	chr2:114647822-114647838 chr2:114647998-114648014
20	HCFC1	chr2:114646720-114649221	Hela-S3	cervix:	n/a	n/a
21	STAT3	chr2:114648870-114649304	MCF10A-Er-Src	breast:	n/a	chr2:114649127-114649138 chr2:114649129-114649137
22	POLR2A	chr2:114646159-114649120	IMR90	lung:	n/a	n/a
23	POLR2A	chr2:114643938-114649214	GM12892	blood:	n/a	n/a
24	JUN	chr2:114646678-114650600	K562	blood:	n/a	chr2:114647000-114647009 chr2:114647383-114647397
25	MXI1	chr2:114646522-114649216	SK-N-SH	brain:	n/a	n/a
26	EP300	chr2:114648284-114649134	GM12878	blood:	n/a	n/a
27	POLR2A	chr2:114645922-114649124	GM18505	blood:	n/a	n/a
28	PML	chr2:114646812-114649136	GM12878	blood:	n/a	n/a
29	ZNF384	chr2:114648142-114649491	GM12878	blood:	n/a	n/a
30	IRF1	chr2:114648226-114650775	K562	blood:	n/a	chr2:114650473-114650480 chr2:114649730-114649744 chr2:114650045-114650059
31	POLR2A	chr2:114649011-114649128	Hela-S3	cervix:	n/a	n/a
32	POLR2A	chr2:114645475-114649449	MCF10A-Er-Src	breast:	n/a	n/a
33	E2F4	chr2:114648369-114649121	MCF10A-Er-Src	breast:	n/a	n/a
34	TBL1XR1	chr2:114648230-114650197	K562	blood:	n/a	n/a
35	MAZ	chr2:114646634-114649174	IMR90	lung:	n/a	n/a
36	RCOR1	chr2:114646934-114649161	K562	blood:	n/a	n/a
37	MYC	chr2:114646872-114649407	K562	blood:	n/a	n/a
38	POLR2A	chr2:114645781-114649125	GM12892	blood:	n/a	n/a
39	ATF2	chr2:114648053-114649147	GM12878	blood:	n/a	n/a
40	ZMIZ1	chr2:114648198-114649106	K562	blood:	n/a	n/a
41	POLR2A	chr2:114646831-114649151	Hela-S3	cervix:	n/a	n/a
42	POLR2A	chr2:114646920-114650720	K562	blood:	n/a	n/a
43	POLR2A	chr2:114643857-114649133	GM12878	blood:	n/a	n/a
44	POLR2A	chr2:114646384-114649189	U87	brain:	n/a	n/a
45	CUX1	chr2:114648451-114649197	K562	blood:	n/a	n/a
46	POLR2A	chr2:114643892-114649129	GM12878	blood:	n/a	n/a
47	STAT3	chr2:114648611-114649754	MCF10A-Er-Src	breast:	n/a	chr2:114649127-114649138 chr2:114649129-114649137
48	POLR2A	chr2:114643857-114649180	GM12878	blood:	n/a	n/a
49	MAFK	chr2:114648368-114649214	K562	blood:	n/a	n/a
50	POLR2A	chr2:114646645-114649169	HUVEC	blood vessel:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:114648278..114650934-chr2:114677225..114679132,2	K562	blood:
2	chr2:114647663..114650657-chr2:114707458..114709843,3	K562	blood:
3	chr2:114510034..114517579-chr2:114643441..114655407,23	MCF-7	breast:
4	chr2:114647663..114650657-chr2:114707458..114709843,2	K562	blood:
5	chr2:114511479..114519908-chr2:114641728..114650266,13	MCF-7	breast:
6	chr2:114648006..114650237-chr2:114689748..114692234,2	K562	blood:
7	chr2:114512680..114516386-chr2:114646106..114650521,15	K562	blood:
8	chr2:114512629..114516386-chr2:114645660..114650521,15	K562	blood:

Variant related genes	Relation type
ENSG00000270019	TF binding region
ENSG00000115091	Chromatin interaction
ENSG00000115084	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10165272	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs10167298	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap]
rs10194568	1.00[CHB][hapmap];0.91[JPT][hapmap]
rs10207551	1.00[CHB][hapmap];0.91[JPT][hapmap]
rs10207785	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs11890727	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap]
rs11899049	0.90[CHB][hapmap]
rs12464791	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap]
rs12618683	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs12711790	0.83[AMR][1000 genomes]
rs12711794	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap]
rs13003655	0.81[AMR][1000 genomes]
rs13405344	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap]
rs13405706	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes]
rs1403402	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes]
rs1467291	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.81[AMR][1000 genomes]
rs1486800	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap]
rs1504042	1.00[CHB][hapmap];0.91[JPT][hapmap]
rs1916201	0.83[AMR][1000 genomes]
rs2140263	0.89[CHB][hapmap]
rs2419080	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs3791737	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes]
rs3791743	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes]
rs4338971	0.83[AMR][1000 genomes]
rs6542177	0.88[CEU][hapmap];0.95[YRI][hapmap];0.82[AMR][1000 genomes]
rs6542178	0.82[AMR][1000 genomes]
rs6542181	0.83[AMR][1000 genomes]
rs6542182	0.83[AMR][1000 genomes]
rs6720853	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6723415	0.83[AMR][1000 genomes]
rs6726327	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap]
rs6734839	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes]
rs6738134	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap]
rs6740934	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes]
rs6743651	1.00[CHB][hapmap]
rs6761646	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs7567097	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes]
rs7582072	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap]
rs7603501	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs7603764	0.83[AMR][1000 genomes]
rs9308686	0.82[AMR][1000 genomes]
rs996514	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes]
rs996515	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AMR][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	esv3379758	chr2:114646832-114649180	Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	n/a

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:114644600-114649600	Active TSS	HUES6 Cell Line	embryonic stem cell
2	chr2:114645400-114649800	Active TSS	GM12878-XiMat	blood
3	chr2:114645800-114649600	Active TSS	iPS-20b Cell Line	embryonic stem cell
4	chr2:114646000-114649200	Active TSS	H9 Cell Line	embryonic stem cell
5	chr2:114646000-114649800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr2:114646000-114650000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr2:114646200-114649200	Active TSS	Fetal Kidney	kidney
8	chr2:114646200-114649400	Active TSS	H1 Cell Line	embryonic stem cell
9	chr2:114646200-114649400	Active TSS	Pancreatic Islets	Pancreatic Islet
10	chr2:114646400-114649200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
11	chr2:114646400-114649200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
12	chr2:114646400-114649200	Active TSS	Fetal Muscle Trunk	muscle
13	chr2:114646400-114649400	Active TSS	Colonic Mucosa	Colon
14	chr2:114646400-114649800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr2:114646400-114649800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr2:114646400-114650000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr2:114646400-114650000	Active TSS	Psoas Muscle	Psoas
18	chr2:114646400-114650000	Active TSS	HSMM	muscle
19	chr2:114646400-114650200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr2:114646400-114650800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr2:114646600-114649200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr2:114646600-114649200	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr2:114646600-114649200	Active TSS	Brain Angular Gyrus	brain
24	chr2:114646600-114649200	Active TSS	Brain Inferior Temporal Lobe	brain
25	chr2:114646600-114649200	Active TSS	Fetal Lung	lung
26	chr2:114646600-114649200	Active TSS	Small Intestine	intestine
27	chr2:114646600-114649200	Active TSS	Hela-S3	cervix
28	chr2:114646600-114649400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr2:114646600-114649400	Active TSS	HUES48 Cell Line	embryonic stem cell
30	chr2:114646600-114649400	Active TSS	iPS-18 Cell Line	embryonic stem cell
31	chr2:114646600-114649600	Active TSS	iPS-15b Cell Line	embryonic stem cell
32	chr2:114646600-114649600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr2:114646600-114649600	Active TSS	Muscle Satellite Cultured Cells	--
34	chr2:114646600-114649600	Active TSS	Colon Smooth Muscle	Colon
35	chr2:114646600-114649600	Active TSS	Duodenum Mucosa	Duodenum
36	chr2:114646600-114649600	Active TSS	NH-A	brain
37	chr2:114646600-114649600	Active TSS	NHDF-Ad	bronchial
38	chr2:114646600-114649800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr2:114646600-114649800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr2:114646600-114649800	Active TSS	NHLF	lung
41	chr2:114646600-114650000	Active TSS	ES-I3 Cell Line	embryonic stem cell
42	chr2:114646600-114650000	Active TSS	Rectal Mucosa Donor 29	rectum
43	chr2:114646600-114650000	Active TSS	Right Atrium	heart
44	chr2:114646600-114650000	Active TSS	HMEC	breast
45	chr2:114646600-114650000	Active TSS	K562	blood
46	chr2:114646600-114650200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr2:114646600-114650200	Active TSS	Right Ventricle	heart
48	chr2:114646600-114651000	Active TSS	Breast Myoepithelial Primary Cells	Breast
49	chr2:114646800-114649400	Active TSS	Primary T killer memory cells from peripheral blood	blood
50	chr2:114646800-114649400	Active TSS	Duodenum Smooth Muscle	Duodenum

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