Variant report

Variant	rs12200499
Chromosome Location	chr6:119256608-119256609
allele	G/T
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	chr6:119255359-119256710	PFSK-1	brain:	n/a	n/a
2	POLR2A	chr6:119255530-119256664	GM19193	blood:	n/a	n/a
3	MAZ	chr6:119255108-119256825	IMR90	lung:	n/a	chr6:119256174-119256185 chr6:119256176-119256183 chr6:119256175-119256185 chr6:119256175-119256184
4	POLR2A	chr6:119255588-119256630	GM12891	blood:	n/a	n/a
5	TRIM28	chr6:119255785-119256712	K562	blood:	n/a	n/a
6	TCF7L2	chr6:119255792-119256653	Hela-S3	cervix:	n/a	n/a
7	TAF1	chr6:119255525-119256666	ECC-1	luminal epithelium:	n/a	n/a
8	POLR2A	chr6:119255637-119256658	HUVEC	blood vessel:	n/a	n/a
9	NR2F2	chr6:119255605-119256835	K562	blood:	n/a	n/a
10	PML	chr6:119255563-119256669	K562	blood:	n/a	n/a
11	RCOR1	chr6:119255486-119256634	K562	blood:	n/a	n/a
12	TEAD4	chr6:119255432-119256697	K562	blood:	n/a	n/a
13	SIN3AK20	chr6:119255468-119256686	MCF-7	breast:	n/a	n/a
14	IRF1	chr6:119255708-119256684	K562	blood:	n/a	chr6:119256399-119256413
15	TFAP2C	chr6:119255612-119256645	Hela-S3	cervix:	n/a	n/a
16	POLR2A	chr6:119255452-119256707	GM18505	blood:	n/a	n/a
17	POLR2A	chr6:119255561-119256673	PANC-1	pancreas:	n/a	n/a
18	POLR2A	chr6:119255394-119256658	K562	blood:	n/a	n/a
19	POLR2A	chr6:119255530-119256777	U87	brain:	n/a	n/a
20	EP300	chr6:119255771-119256703	K562	blood:	n/a	chr6:119256199-119256215
21	EGR1	chr6:119255469-119256617	HCT-116	colon:	n/a	chr6:119255749-119255762 chr6:119255749-119255762 chr6:119255725-119255739
22	MAZ	chr6:119255415-119256719	GM12878	blood:	n/a	chr6:119256174-119256185 chr6:119256176-119256183 chr6:119256175-119256185 chr6:119256175-119256184
23	MYBL2	chr6:119255629-119256821	HepG2	liver:	n/a	n/a
24	RCOR1	chr6:119255414-119256662	Hela-S3	cervix:	n/a	n/a
25	TAF1	chr6:119255636-119256617	H1-hESC	embryonic stem cell:	n/a	n/a
26	MYBL2	chr6:119255554-119256742	HepG2	liver:	n/a	n/a
27	POLR2A	chr6:119255532-119256610	K562	blood:	n/a	n/a
28	TAF1	chr6:119255927-119256648	H1-hESC	embryonic stem cell:	n/a	n/a
29	NFATC1	chr6:119255722-119256633	GM12878	blood:	n/a	n/a
30	JUND	chr6:119255695-119256618	K562	blood:	n/a	n/a
31	NRF1	chr6:119255650-119256719	SK-N-SH	brain:	n/a	n/a
32	POLR2A	chr6:119255447-119256660	GM19099	blood:	n/a	n/a
33	POLR2A	chr6:119255592-119256656	K562	blood:	n/a	n/a
34	HEY1	chr6:119255550-119256648	K562	blood:	n/a	n/a
35	POLR2A	chr6:119255566-119256613	GM12891	blood:	n/a	n/a
36	MYC	chr6:119255382-119256636	NB4	blood:	n/a	chr6:119256174-119256185 chr6:119256176-119256183 chr6:119256175-119256185 chr6:119256175-119256184
37	ZMIZ1	chr6:119255621-119256611	K562	blood:	n/a	n/a
38	POLR2A	chr6:119255451-119256652	Raji	blood:	n/a	n/a
39	POLR2A	chr6:119255425-119256627	GM12892	blood:	n/a	n/a
40	POLR2A	chr6:119255292-119256608	Hela-S3	cervix:	n/a	n/a
41	POLR2A	chr6:119255643-119256834	MCF10A-Er-Src	breast:	n/a	n/a
42	POLR2A	chr6:119255462-119256635	GM18951	blood:	n/a	n/a
43	POLR2A	chr6:119256108-119256682	SK-N-SH	brain:	n/a	n/a
44	POLR2A	chr6:119255666-119256626	GM12892	blood:	n/a	n/a
45	MXI1	chr6:119255355-119256679	IMR90	lung:	n/a	n/a
46	POU2F2	chr6:119255904-119256611	GM12891	blood:	n/a	chr6:119256152-119256164
47	POLR2A	chr6:119255652-119256639	HepG2	liver:	n/a	n/a
48	RUNX3	chr6:119255477-119256646	GM12878	blood:	n/a	n/a
49	POLR2A	chr6:119255463-119256652	GM12892	blood:	n/a	n/a
50	POLR2A	chr6:119255545-119256687	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:119213694..119219544-chr6:119251621..119258172,21	K562	blood:
2	chr4:79472622..79473237-chr6:119256049..119256758,2	HCT-116	colon:
3	chr6:119253156..119256806-chr6:119394976..119399977,7	K562	blood:
4	chr6:119256349..119258481-chr6:119264695..119266812,2	K562	blood:
5	chr6:119256205..119257932-chr6:119293855..119296677,2	K562	blood:
6	chr6:119213036..119217484-chr6:119254311..119257675,9	MCF-7	breast:
7	chr6:119242613..119249110-chr6:119251513..119257145,6	MCF-7	breast:
8	chr6:119256106..119257947-chr6:119468580..119471034,2	K562	blood:
9	chr6:119255727..119258203-chr6:119400226..119402388,2	K562	blood:
10	chr6:119214552..119219906-chr6:119253918..119257622,8	MCF-7	breast:
11	chr6:119253238..119258280-chr6:119398045..119402661,8	K562	blood:
12	chr6:119256460..119259122-chr6:119259921..119263121,4	K562	blood:
13	chr6:119213105..119220728-chr6:119253299..119257962,22	K562	blood:
14	chr1:149223435..149224292-chr6:119255876..119256729,2	HCT-116	colon:
15	chr15:90708735..90709594-chr6:119255785..119256642,2	HCT-116	colon:
16	chr10:74927354..74928318-chr6:119255751..119256642,2	NB4	blood:

Variant related genes	Relation type
MCM9	TF binding region
ENSG00000138286	Chromatin interaction
ENSG00000111875	Chromatin interaction
ENSG00000138772	Chromatin interaction
ENSG00000122882	Chromatin interaction
ENSG00000111877	Chromatin interaction
ENSG00000240470	Chromatin interaction
ENSG00000206737	Chromatin interaction
ENSG00000111879	Chromatin interaction

Extended variants
information (count: 97 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:95)

rs_ID	r²[population]
rs10080855	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10456919	0.81[AMR][1000 genomes]
rs1087453	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1087454	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1087455	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11153785	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12190974	0.91[AMR][1000 genomes]
rs12191490	0.83[ASN][1000 genomes]
rs12191819	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12194515	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12195153	0.91[AMR][1000 genomes]
rs12196440	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12197931	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12203353	0.85[AFR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12203542	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12206826	0.97[ASN][1000 genomes]
rs12210027	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12212179	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12214434	0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12216519	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1321836	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1342793	0.91[AMR][1000 genomes]
rs1407205	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1407206	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1418712	0.86[AMR][1000 genomes]
rs1539434	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1775619	0.91[AMR][1000 genomes]
rs2295709	0.82[ASN][1000 genomes]
rs2357022	0.86[AMR][1000 genomes]
rs2782574	0.86[AMR][1000 genomes]
rs2797355	0.91[AMR][1000 genomes]
rs284914	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs284915	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs284916	0.83[ASN][1000 genomes]
rs284918	0.96[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs284920	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs376225	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3798594	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3798595	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3798599	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs388987	0.83[AFR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs409849	0.84[ASN][1000 genomes]
rs41292550	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41292554	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4946384	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs55810806	0.81[AMR][1000 genomes]
rs56794995	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56895036	0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6935641	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6937499	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs706971	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs706978	0.91[AMR][1000 genomes]
rs72966811	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs72966851	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72966873	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72966896	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72970448	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs768995	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs768996	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7768348	0.86[AMR][1000 genomes]
rs794250	0.91[AMR][1000 genomes]
rs794252	0.91[AMR][1000 genomes]
rs794253	0.91[AMR][1000 genomes]
rs794254	0.91[AMR][1000 genomes]
rs794259	0.91[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs794606	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs794607	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs794608	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs794611	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs797017	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs811201	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs811584	0.81[AMR][1000 genomes]
rs9320673	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9374757	0.80[ASN][1000 genomes]
rs9387609	0.80[ASN][1000 genomes]
rs9481862	0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9481867	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9481868	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9481869	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9481870	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9481871	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9481872	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9481877	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9481878	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9489530	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9489531	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9489535	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9489536	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9489537	0.97[ASN][1000 genomes]
rs9489539	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9489540	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9489541	0.87[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs9489543	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9489544	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9489547	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv16596	chr6:119251007-119272087	Active TSS Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases
2	nsv437523	chr6:119251971-119260280	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:119254000-119257400	Active TSS	GM12878-XiMat	blood
2	chr6:119254600-119257000	Active TSS	Fetal Intestine Large	intestine
3	chr6:119255000-119257000	Active TSS	H1 Cell Line	embryonic stem cell
4	chr6:119255000-119257000	Active TSS	HMEC	breast
5	chr6:119255000-119257200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr6:119255000-119257200	Active TSS	Stomach Smooth Muscle	stomach
7	chr6:119255200-119256800	Active TSS	H9 Cell Line	embryonic stem cell
8	chr6:119255200-119256800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr6:119255200-119256800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr6:119255200-119256800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr6:119255200-119256800	Active TSS	Aorta	Aorta
12	chr6:119255200-119256800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
13	chr6:119255200-119256800	Active TSS	Fetal Muscle Trunk	muscle
14	chr6:119255200-119256800	Active TSS	Fetal Stomach	stomach
15	chr6:119255200-119256800	Active TSS	Right Atrium	heart
16	chr6:119255200-119256800	Active TSS	Right Ventricle	heart
17	chr6:119255200-119256800	Active TSS	Stomach Mucosa	stomach
18	chr6:119255200-119256800	Active TSS	A549	lung
19	chr6:119255200-119257000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
20	chr6:119255200-119257000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr6:119255200-119257000	Active TSS	HSMMtube	muscle
22	chr6:119255200-119257200	Active TSS	HUES48 Cell Line	embryonic stem cell
23	chr6:119255200-119257400	Active TSS	HSMM	muscle
24	chr6:119255400-119256800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr6:119255400-119256800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr6:119255400-119256800	Active TSS	iPS-15b Cell Line	embryonic stem cell
27	chr6:119255400-119256800	Active TSS	iPS-20b Cell Line	embryonic stem cell
28	chr6:119255400-119256800	Active TSS	Primary T cells fromperipheralblood	blood
29	chr6:119255400-119256800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr6:119255400-119256800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr6:119255400-119256800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr6:119255400-119256800	Active TSS	Brain Anterior Caudate	brain
33	chr6:119255400-119256800	Active TSS	Brain Germinal Matrix	brain
34	chr6:119255400-119256800	Active TSS	Brain Hippocampus Middle	brain
35	chr6:119255400-119256800	Active TSS	Brain Inferior Temporal Lobe	brain
36	chr6:119255400-119256800	Active TSS	Brain Substantia Nigra	brain
37	chr6:119255400-119256800	Active TSS	Colonic Mucosa	Colon
38	chr6:119255400-119256800	Active TSS	Ovary	ovary
39	chr6:119255400-119256800	Active TSS	Thymus	Thymus
40	chr6:119255400-119257000	Active TSS	ES-I3 Cell Line	embryonic stem cell
41	chr6:119255400-119257000	Active TSS	Breast Myoepithelial Primary Cells	Breast
42	chr6:119255400-119257000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr6:119255400-119257000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr6:119255400-119257000	Active TSS	Fetal Intestine Small	intestine
45	chr6:119255400-119257000	Active TSS	Pancreatic Islets	Pancreatic Islet
46	chr6:119255400-119257000	Active TSS	Fetal Muscle Leg	muscle
47	chr6:119255400-119257000	Active TSS	K562	blood
48	chr6:119255400-119257000	Active TSS	NHDF-Ad	bronchial
49	chr6:119255400-119257200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr6:119255400-119257400	Active TSS	Hela-S3	cervix

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