Variant report

Variant	rs996515
Chromosome Location	chr2:114648900-114648901
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	chr2:114646525-114649045	H1-hESC	embryonic stem cell:	n/a	n/a
2	SIN3AK20	chr2:114646869-114648995	MCF-7	breast:	n/a	n/a
3	POLR2A	chr2:114648793-114649128	U87	brain:	n/a	n/a
4	SRF	chr2:114648100-114649094	MCF-7	breast:	n/a	chr2:114648658-114648673 chr2:114648659-114648672 chr2:114648661-114648670 chr2:114648657-114648671 chr2:114648661-114648672 chr2:114648660-114648671 chr2:114648659-114648670 chr2:114648657-114648674 chr2:114648656-114648674
5	STAT3	chr2:114648894-114649291	MCF10A-Er-Src	breast:	n/a	chr2:114649127-114649138 chr2:114649129-114649137
6	IRF1	chr2:114648308-114650459	K562	blood:	n/a	chr2:114649730-114649744 chr2:114650045-114650059
7	POLR2A	chr2:114646884-114649051	GM12892	blood:	n/a	n/a
8	GTF2F1	chr2:114648354-114648974	K562	blood:	n/a	n/a
9	NFATC1	chr2:114648225-114649198	GM12878	blood:	n/a	n/a
10	POLR2A	chr2:114643857-114649205	GM12891	blood:	n/a	n/a
11	NFIC	chr2:114648229-114648978	GM12878	blood:	n/a	n/a
12	CUX1	chr2:114648269-114648924	GM12878	blood:	n/a	n/a
13	POLR2A	chr2:114646950-114649014	PBDE	blood:	n/a	n/a
14	BCLAF1	chr2:114646904-114649154	GM12878	blood:	n/a	chr2:114648180-114648193 chr2:114648094-114648103 chr2:114647523-114647536 chr2:114648262-114648271
15	POLR2A	chr2:114643825-114649166	GM12892	blood:	n/a	n/a
16	MXI1	chr2:114648230-114649039	K562	blood:	n/a	n/a
17	TBP	chr2:114646842-114649197	K562	blood:	n/a	n/a
18	EP300	chr2:114648171-114649246	K562	blood:	n/a	chr2:114649141-114649155
19	TAF1	chr2:114646866-114648921	GM12878	blood:	n/a	n/a
20	POLR2A	chr2:114643910-114650805	GM12878	blood:	n/a	n/a
21	SRF	chr2:114648341-114648919	ECC-1	luminal epithelium:	n/a	chr2:114648658-114648673 chr2:114648659-114648672 chr2:114648661-114648670 chr2:114648657-114648671 chr2:114648661-114648672 chr2:114648660-114648671 chr2:114648659-114648670 chr2:114648657-114648674 chr2:114648656-114648674
22	POLR2A	chr2:114646291-114649087	K562	blood:	n/a	n/a
23	POLR2A	chr2:114646562-114649092	GM18951	blood:	n/a	n/a
24	POLR2A	chr2:114646596-114649078	Raji	blood:	n/a	n/a
25	MYC	chr2:114646952-114649094	K562	blood:	n/a	n/a
26	FOXM1	chr2:114648024-114648957	GM12878	blood:	n/a	n/a
27	TBP	chr2:114648281-114649217	Hela-S3	cervix:	n/a	n/a
28	POLR2A	chr2:114646970-114649046	GM12891	blood:	n/a	n/a
29	POLR2A	chr2:114646939-114649035	K562	blood:	n/a	n/a
30	POLR2A	chr2:114646964-114648999	GM18526	blood:	n/a	n/a
31	STAT5A	chr2:114646934-114649085	GM12878	blood:	n/a	chr2:114647957-114647969 chr2:114648251-114648262 chr2:114648155-114648167 chr2:114647915-114647927
32	CHD2	chr2:114648070-114649105	K562	blood:	n/a	n/a
33	STAT1	chr2:114648366-114649056	GM12878	blood:	n/a	n/a
34	FOXM1	chr2:114646508-114648927	GM12878	blood:	n/a	n/a
35	POLR2A	chr2:114646638-114649048	GM12891	blood:	n/a	n/a
36	POLR2A	chr2:114646736-114648915	HUVEC	blood vessel:	n/a	n/a
37	RELA	chr2:114647000-114648905	GM19193	blood:	n/a	chr2:114647381-114647390 chr2:114647381-114647390
38	POLR2A	chr2:114644799-114649079	HepG2	liver:	n/a	n/a
39	TBP	chr2:114648263-114649183	GM12878	blood:	n/a	n/a
40	JUND	chr2:114646941-114649195	K562	blood:	n/a	chr2:114647000-114647009 chr2:114647383-114647397
41	MXI1	chr2:114646608-114649272	IMR90	lung:	n/a	n/a
42	MAZ	chr2:114646541-114649026	K562	blood:	n/a	n/a
43	ZNF384	chr2:114648188-114649905	K562	blood:	n/a	n/a
44	RUNX3	chr2:114648098-114648962	GM12878	blood:	n/a	n/a
45	MAZ	chr2:114646746-114649029	GM12878	blood:	n/a	n/a
46	CHD1	chr2:114646374-114649786	GM12878	blood:	n/a	n/a
47	SIN3A	chr2:114647043-114648984	GM12878	blood:	n/a	chr2:114648179-114648192
48	SRF	chr2:114648194-114649014	ECC-1	luminal epithelium:	n/a	chr2:114648658-114648673 chr2:114648659-114648672 chr2:114648661-114648670 chr2:114648657-114648671 chr2:114648661-114648672 chr2:114648660-114648671 chr2:114648659-114648670 chr2:114648657-114648674 chr2:114648656-114648674
49	BHLHE40	chr2:114647090-114649118	GM12878	blood:	n/a	chr2:114647822-114647838 chr2:114647998-114648014
50	HCFC1	chr2:114646720-114649221	Hela-S3	cervix:	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	chr2:114648161..114648926-chr6:27099888..27100517,2	Hela-S3	cervix:
7	chr2:114648006..114650237-chr2:114689748..114692234,2	K562	blood:
8	chr2:114512680..114516386-chr2:114646106..114650521,15	K562	blood:
9	chr2:114512629..114516386-chr2:114645660..114650521,15	K562	blood:

Variant related genes	Relation type
ENSG00000270019	TF binding region
ENSG00000115091	Chromatin interaction
ENSG00000115084	Chromatin interaction
ENSG00000124635	Chromatin interaction

Extended variants
information (count: 82 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs10165272	1.00[CHB][hapmap];0.87[JPT][hapmap];0.94[ASN][1000 genomes]
rs10167298	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10177263	0.94[ASN][1000 genomes]
rs10194568	1.00[CHB][hapmap];0.91[JPT][hapmap];0.92[ASN][1000 genomes]
rs10195630	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10201959	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10202134	0.94[ASN][1000 genomes]
rs10207551	1.00[CHB][hapmap];0.91[JPT][hapmap];0.94[ASN][1000 genomes]
rs10207785	1.00[CHB][hapmap];0.91[JPT][hapmap];0.94[ASN][1000 genomes]
rs10210324	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1022412	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11123218	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11887418	0.91[ASN][1000 genomes]
rs11887772	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11889821	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11890727	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11893418	0.94[ASN][1000 genomes]
rs11896388	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11898729	0.85[ASN][1000 genomes]
rs11899049	0.90[CHB][hapmap];0.82[ASN][1000 genomes]
rs12464791	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12466566	0.83[ASN][1000 genomes]
rs12466572	0.93[ASN][1000 genomes]
rs12613877	0.93[ASN][1000 genomes]
rs12618683	1.00[CHB][hapmap];0.91[JPT][hapmap];0.93[ASN][1000 genomes]
rs12711790	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12711794	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13003655	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs13387553	0.91[ASN][1000 genomes]
rs13388876	0.85[ASN][1000 genomes]
rs13396086	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13396561	0.90[ASN][1000 genomes]
rs13401311	0.83[ASN][1000 genomes]
rs13405344	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13405706	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13418557	0.90[ASN][1000 genomes]
rs13422248	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1403402	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1467291	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1486800	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1504042	1.00[CHB][hapmap];0.91[JPT][hapmap];0.96[ASN][1000 genomes]
rs17045275	0.85[ASN][1000 genomes]
rs1916201	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1984794	0.84[ASN][1000 genomes]
rs2140263	0.89[CHB][hapmap];0.83[ASN][1000 genomes]
rs2419080	1.00[CHB][hapmap];0.91[JPT][hapmap];0.93[ASN][1000 genomes]
rs28423681	0.83[ASN][1000 genomes]
rs3791737	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3791739	0.96[ASN][1000 genomes]
rs3791743	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4278937	0.98[ASN][1000 genomes]
rs4338971	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55685338	0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs55810358	0.94[ASN][1000 genomes]
rs6542177	0.88[CEU][hapmap];0.95[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6542178	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6542181	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6542182	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6542184	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6542186	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6711858	0.96[ASN][1000 genomes]
rs6720853	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs6723415	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6726327	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6729412	0.91[ASN][1000 genomes]
rs6734839	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6738134	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6740934	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6743651	1.00[CHB][hapmap];0.89[ASN][1000 genomes]
rs6750503	0.90[ASN][1000 genomes]
rs6760347	0.84[ASN][1000 genomes]
rs6761646	1.00[CHB][hapmap];0.87[JPT][hapmap];0.86[ASN][1000 genomes]
rs7567097	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7582072	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7585468	0.98[ASN][1000 genomes]
rs7595941	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7603501	1.00[CHB][hapmap];0.91[JPT][hapmap];0.94[ASN][1000 genomes]
rs7603764	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9308686	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs996513	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes]
rs996514	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	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:126 , 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	chr2:114646000-114649000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr2:114646000-114649200	Active TSS	H9 Cell Line	embryonic stem cell
6	chr2:114646000-114649800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr2:114646000-114650000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr2:114646200-114649000	Active TSS	Stomach Mucosa	stomach
9	chr2:114646200-114649200	Active TSS	Fetal Kidney	kidney
10	chr2:114646200-114649400	Active TSS	H1 Cell Line	embryonic stem cell
11	chr2:114646200-114649400	Active TSS	Pancreatic Islets	Pancreatic Islet
12	chr2:114646400-114649200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
13	chr2:114646400-114649200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
14	chr2:114646400-114649200	Active TSS	Fetal Muscle Trunk	muscle
15	chr2:114646400-114649400	Active TSS	Colonic Mucosa	Colon
16	chr2:114646400-114649800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr2:114646400-114649800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr2:114646400-114650000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr2:114646400-114650000	Active TSS	Psoas Muscle	Psoas
20	chr2:114646400-114650000	Active TSS	HSMM	muscle
21	chr2:114646400-114650200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr2:114646400-114650800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr2:114646600-114649000	Active TSS	Ovary	ovary
24	chr2:114646600-114649000	Active TSS	Placenta Amnion	Placenta Amnion
25	chr2:114646600-114649200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr2:114646600-114649200	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr2:114646600-114649200	Active TSS	Brain Angular Gyrus	brain
28	chr2:114646600-114649200	Active TSS	Brain Inferior Temporal Lobe	brain
29	chr2:114646600-114649200	Active TSS	Fetal Lung	lung
30	chr2:114646600-114649200	Active TSS	Small Intestine	intestine
31	chr2:114646600-114649200	Active TSS	Hela-S3	cervix
32	chr2:114646600-114649400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr2:114646600-114649400	Active TSS	HUES48 Cell Line	embryonic stem cell
34	chr2:114646600-114649400	Active TSS	iPS-18 Cell Line	embryonic stem cell
35	chr2:114646600-114649600	Active TSS	iPS-15b Cell Line	embryonic stem cell
36	chr2:114646600-114649600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr2:114646600-114649600	Active TSS	Muscle Satellite Cultured Cells	--
38	chr2:114646600-114649600	Active TSS	Colon Smooth Muscle	Colon
39	chr2:114646600-114649600	Active TSS	Duodenum Mucosa	Duodenum
40	chr2:114646600-114649600	Active TSS	NH-A	brain
41	chr2:114646600-114649600	Active TSS	NHDF-Ad	bronchial
42	chr2:114646600-114649800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr2:114646600-114649800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr2:114646600-114649800	Active TSS	NHLF	lung
45	chr2:114646600-114650000	Active TSS	ES-I3 Cell Line	embryonic stem cell
46	chr2:114646600-114650000	Active TSS	Rectal Mucosa Donor 29	rectum
47	chr2:114646600-114650000	Active TSS	Right Atrium	heart
48	chr2:114646600-114650000	Active TSS	HMEC	breast
49	chr2:114646600-114650000	Active TSS	K562	blood
50	chr2:114646600-114650200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin

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