Variant report

Variant	rs17118333
Chromosome Location	chr12:56552826-56552827
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	chr12:56551094-56558885	SK-N-SH	brain:	n/a	n/a
2	POLR2A	chr12:56552592-56554130	HepG2	liver:	n/a	n/a
3	POLR2A	chr12:56551096-56559842	GM12878	blood:	n/a	n/a
4	TCF12	chr12:56550943-56553118	ECC-1	luminal epithelium:	n/a	n/a
5	POLR2A	chr12:56551899-56559978	HUVEC	blood vessel:	n/a	n/a
6	POLR2A	chr12:56551937-56557019	Hela-S3	cervix:	n/a	n/a
7	POLR2A	chr12:56550969-56558589	GM12892	blood:	n/a	n/a
8	SRF	chr12:56552804-56553213	GM12878	blood:	n/a	chr12:56553044-56553058 chr12:56553040-56553058 chr12:56553042-56553055 chr12:56553039-56553053 chr12:56553041-56553056 chr12:56553044-56553053 chr12:56553042-56553055 chr12:56553042-56553053 chr12:56553039-56553057 chr12:56553043-56553054 chr12:56553044-56553055 chr12:56553039-56553057 chr12:56553043-56553057 chr12:56553040-56553057
9	POLR2A	chr12:56551944-56557093	GM12892	blood:	n/a	n/a
10	POLR2A	chr12:56551911-56556101	SK-N-SH	brain:	n/a	n/a
11	IRF1	chr12:56551513-56552858	K562	blood:	n/a	chr12:56552640-56552654 chr12:56552073-56552082
12	POLR2A	chr12:56551250-56558611	U87	brain:	n/a	n/a
13	CEBPD	chr12:56551920-56553357	K562	blood:	n/a	n/a
14	STAT5A	chr12:56551925-56553724	GM12878	blood:	n/a	chr12:56552662-56552670 chr12:56552231-56552239
15	JUND	chr12:56552646-56555329	A549	lung:	n/a	n/a
16	POLR2A	chr12:56551168-56556161	H1-hESC	embryonic stem cell:	n/a	n/a
17	POLR2A	chr12:56551896-56556539	HCT-116	colon:	n/a	n/a
18	POLR2A	chr12:56551408-56556564	K562	blood:	n/a	n/a
19	POLR2A	chr12:56550856-56557007	HepG2	liver:	n/a	n/a
20	CHD1	chr12:56551947-56555381	IMR90	lung:	n/a	chr12:56552251-56552261 chr12:56554880-56554890
21	POLR2A	chr12:56551816-56553252	HepG2	liver:	n/a	n/a
22	POLR2A	chr12:56551957-56553119	HEK293	kidney:	n/a	n/a
23	POLR2A	chr12:56551369-56560498	MCF10A-Er-Src	breast:	n/a	n/a
24	POLR2A	chr12:56551498-56553336	HepG2	liver:	n/a	n/a
25	SRF	chr12:56552614-56553330	ECC-1	luminal epithelium:	n/a	chr12:56553044-56553058 chr12:56553040-56553058 chr12:56553042-56553055 chr12:56553039-56553053 chr12:56553041-56553056 chr12:56553044-56553053 chr12:56553042-56553055 chr12:56553042-56553053 chr12:56553039-56553057 chr12:56553043-56553054 chr12:56553044-56553055 chr12:56553039-56553057 chr12:56553043-56553057 chr12:56553040-56553057
26	POLR2A	chr12:56551123-56558578	Hela-S3	cervix:	n/a	n/a
27	TBP	chr12:56551246-56553360	H1-hESC	embryonic stem cell:	n/a	n/a
28	SIN3AK20	chr12:56551943-56553159	A549	lung:	n/a	n/a
29	POLR2A	chr12:56551053-56559864	GM12891	blood:	n/a	n/a
30	TAF1	chr12:56550881-56553216	H1-hESC	embryonic stem cell:	n/a	n/a
31	POLR2A	chr12:56551393-56557009	K562	blood:	n/a	n/a
32	POLR2A	chr12:56550960-56557121	K562	blood:	n/a	n/a
33	YY1	chr12:56551916-56552980	GM12878	blood:	n/a	chr12:56552181-56552193 chr12:56552175-56552195 chr12:56552637-56552647
34	BCL3	chr12:56551157-56556978	A549	lung:	n/a	chr12:56553213-56553222 chr12:56554315-56554324 chr12:56552652-56552661 chr12:56554170-56554179
35	ETS1	chr12:56552559-56553226	A549	lung:	n/a	n/a
36	POLR2A	chr12:56551331-56558611	U87	brain:	n/a	n/a
37	POLR2A	chr12:56551292-56558563	HepG2	liver:	n/a	n/a
38	JUN	chr12:56551927-56552883	K562	blood:	n/a	chr12:56552095-56552104 chr12:56552091-56552104
39	RELA	chr12:56551074-56553311	GM18505	blood:	n/a	n/a
40	POLR2A	chr12:56550957-56556171	H1-hESC	embryonic stem cell:	n/a	n/a
41	TAF1	chr12:56550931-56553354	ECC-1	luminal epithelium:	n/a	n/a
42	POLR2A	chr12:56551237-56556498	GM12878	blood:	n/a	n/a
43	ATF2	chr12:56551843-56553050	GM12878	blood:	n/a	n/a
44	CTCF	chr12:56551234-56553345	SK-N-SH	brain:	n/a	n/a
45	POLR2A	chr12:56551158-56552967	Raji	blood:	n/a	n/a
46	POLR2A	chr12:56551288-56555232	K562	blood:	n/a	n/a
47	PML	chr12:56551898-56553609	K562	blood:	n/a	n/a
48	TEAD4	chr12:56551099-56553461	ECC-1	luminal epithelium:	n/a	n/a
49	POLR2A	chr12:56551925-56553906	SK-N-MC	brain:	n/a	n/a
50	POLR2A	chr12:56551184-56558544	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:56550673..56553390-chr18:11908435..11911361,2	MCF-7	breast:
2	chr12:56471332..56475358-chr12:56550630..56554454,5	MCF-7	breast:
3	chr12:56434374..56437071-chr12:56550642..56553636,4	MCF-7	breast:
4	chr12:56507747..56515530-chr12:56549896..56559767,36	MCF-7	breast:
5	chr12:56209755..56212447-chr12:56551879..56553739,2	MCF-7	breast:
6	chr1:144533652..144534300-chr12:56552105..56553643,4	Hela-S3	cervix:
7	chr1:171711044..171711901-chr12:56552077..56552933,3	Hela-S3	cervix:
8	chr12:56552225..56553095-chr6:89789379..89790360,2	Hela-S3	cervix:
9	chr12:56434567..56436421-chr12:56551645..56554362,3	MCF-7	breast:
10	chr12:56552050..56552857-chrX:53710656..53711232,2	Hela-S3	cervix:
11	chr1:954847..956980-chr12:56550477..56552880,2	MCF-7	breast:
12	chr12:56551653..56553251-chr6:27776259..27779166,2	MCF-7	breast:
13	chr12:56551311..56554280-chr12:56613250..56616267,3	MCF-7	breast:
14	chr12:56531568..56534983-chr12:56550075..56554520,6	MCF-7	breast:
15	chr12:56480457..56482671-chr12:56551431..56553649,2	MCF-7	breast:
16	chr12:56516279..56526040-chr12:56550254..56554953,37	MCF-7	breast:
17	chr12:56549760..56554422-chr12:56650832..56654963,6	MCF-7	breast:
18	chr11:61734073..61736809-chr12:56551929..56554147,2	MCF-7	breast:
19	chr12:56552187..56553182-chr6:74230104..74231036,2	Hela-S3	cervix:
20	chr12:56434092..56435829-chr12:56551661..56553282,2	K562	blood:
21	chr12:56552697..56553653-chr19:46145176..46145906,2	Hela-S3	cervix:
22	chr12:56536501..56538802-chr12:56552198..56554579,2	MCF-7	breast:
23	chr12:56552563..56553324-chr9:114245972..114246681,2	Hela-S3	cervix:
24	chr12:56529351..56534783-chr12:56551483..56555184,6	MCF-7	breast:
25	chr12:56550178..56557145-chr12:56575233..56584234,22	MCF-7	breast:
26	chr12:56497819..56500036-chr12:56550546..56554351,4	MCF-7	breast:
27	chr12:56473103..56475967-chr12:56549779..56553082,5	MCF-7	breast:
28	chr12:56552000..56552966-chr5:141488158..141488709,2	Hela-S3	cervix:
29	chr12:56551520..56554242-chr12:56650975..56653538,2	MCF-7	breast:
30	chr11:82996671..82997589-chr12:56552142..56552833,2	Hela-S3	cervix:
31	chr12:56508092..56528020-chr12:56536122..56568603,201	MCF-7	breast:
32	chr12:56475818..56478694-chr12:56550865..56553540,2	MCF-7	breast:
33	chr12:56549752..56553222-chr12:56691115..56694737,3	K562	blood:
34	chr12:53843995..53846384-chr12:56551140..56553594,2	MCF-7	breast:
35	chr12:56552406..56553057-chr16:89988913..89989513,2	Hela-S3	cervix:
36	chr1:180991460..180992148-chr12:56552600..56553325,2	Hela-S3	cervix:
37	chr12:56551730..56554656-chr12:57027945..57032236,3	K562	blood:
38	chr12:56551787..56553694-chr12:56657880..56660758,2	MCF-7	breast:
39	chr12:56223309..56224865-chr12:56552081..56554400,2	MCF-7	breast:
40	chr12:56549935..56553580-chr12:56615062..56619140,6	MCF-7	breast:
41	chr12:56552067..56552883-chr15:60771137..60771814,2	Hela-S3	cervix:
42	chr12:56552257..56552852-chr12:125401055..125401855,2	Hela-S3	cervix:
43	chr12:56552243..56552906-chr15:74908074..74908878,2	Hela-S3	cervix:

Variant related genes	Relation type
ENSG00000257809	TF binding region
MYL6	TF binding region
ENSG00000139613	Chromatin interaction
ENSG00000258199	Chromatin interaction
ENSG00000229117	Chromatin interaction
ENSG00000139645	Chromatin interaction
ENSG00000135482	Chromatin interaction
ENSG00000188157	Chromatin interaction
ENSG00000257303	Chromatin interaction
ENSG00000137500	Chromatin interaction
ENSG00000179335	Chromatin interaction
ENSG00000167996	Chromatin interaction
ENSG00000258345	Chromatin interaction
ENSG00000197728	Chromatin interaction
ENSG00000131507	Chromatin interaction
ENSG00000076108	Chromatin interaction
ENSG00000258317	Chromatin interaction
ENSG00000201699	Chromatin interaction
ENSG00000257449	Chromatin interaction
ENSG00000117533	Chromatin interaction
ENSG00000245534	Chromatin interaction
ENSG00000197111	Chromatin interaction
ENSG00000123353	Chromatin interaction
ENSG00000135469	Chromatin interaction
ENSG00000255234	Chromatin interaction
ENSG00000273141	Chromatin interaction
ENSG00000139641	Chromatin interaction
ENSG00000125746	Chromatin interaction
ENSG00000181852	Chromatin interaction
ENSG00000269089	Chromatin interaction
ENSG00000136813	Chromatin interaction
ENSG00000205323	Chromatin interaction
ENSG00000170515	Chromatin interaction
ENSG00000139579	Chromatin interaction
ENSG00000154889	Chromatin interaction
ENSG00000086758	Chromatin interaction
ENSG00000065361	Chromatin interaction
ENSG00000182796	Chromatin interaction
ENSG00000062485	Chromatin interaction
ENSG00000135392	Chromatin interaction
ENSG00000259006	Chromatin interaction
ENSG00000203813	Chromatin interaction
ENSG00000156508	Chromatin interaction
ENSG00000135823	Chromatin interaction
ENSG00000128915	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10747763	1.00[JPT][hapmap]
rs10876878	0.83[ASN][1000 genomes]
rs11171752	0.94[ASN][1000 genomes]
rs11171772	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs11171777	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs11834728	1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12320265	1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs1274502	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs1274503	0.83[ASN][1000 genomes]
rs1405859	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs1689518	1.00[CHD][hapmap]
rs2271188	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs2271190	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2271192	1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2271193	1.00[CHD][hapmap]
rs2277340	1.00[CHD][hapmap]
rs2463365	1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2629451	0.83[ASN][1000 genomes]
rs2629453	1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2695783	1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2695784	1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs28676339	1.00[ASN][1000 genomes]
rs2930788	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2950573	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs3759096	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs3802996	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs3809130	1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4759218	1.00[JPT][hapmap]
rs55887836	0.93[ASN][1000 genomes]
rs56851901	1.00[ASN][1000 genomes]
rs57280585	1.00[ASN][1000 genomes]
rs58009483	0.83[ASN][1000 genomes]
rs58476735	1.00[ASN][1000 genomes]
rs58548156	1.00[ASN][1000 genomes]
rs58663297	1.00[ASN][1000 genomes]
rs59053322	0.83[ASN][1000 genomes]
rs59078852	0.83[ASN][1000 genomes]
rs59966703	0.83[ASN][1000 genomes]
rs60396934	1.00[ASN][1000 genomes]
rs61939011	0.83[ASN][1000 genomes]
rs6581091	1.00[JPT][hapmap]
rs703823	1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs7311008	1.00[JPT][hapmap]
rs7489249	1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs773654	0.83[ASN][1000 genomes]
rs773658	1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs773659	1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs773661	0.83[ASN][1000 genomes]
rs7962107	1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs7967464	0.83[ASN][1000 genomes]
rs7975405	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051961	chr12:56262220-56629427	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	284 gene(s)	inside rSNPs	diseases
2	nsv559011	chr12:56551249-56555022	Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	84 gene(s)	inside rSNPs	diseases
3	nsv559012	chr12:56551249-56555360	Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
4	nsv559013	chr12:56551249-56556389	Active TSS Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Weak transcription Flanking Bivalent TSS/Enh Enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
5	nsv559014	chr12:56551250-56555022	Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	84 gene(s)	inside rSNPs	diseases
6	nsv559015	chr12:56551480-56555022	Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	83 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:56550600-56553000	Active TSS	GM12878-XiMat	blood
2	chr12:56550600-56553200	Active TSS	Fetal Brain Female	brain
3	chr12:56550800-56553000	Active TSS	Brain Anterior Caudate	brain
4	chr12:56550800-56553200	Active TSS	HUES48 Cell Line	embryonic stem cell
5	chr12:56550800-56553200	Active TSS	Fetal Kidney	kidney
6	chr12:56550800-56553200	Active TSS	Rectal Mucosa Donor 29	rectum
7	chr12:56550800-56553200	Active TSS	NHDF-Ad	bronchial
8	chr12:56550800-56553400	Active TSS	ES-I3 Cell Line	embryonic stem cell
9	chr12:56550800-56553400	Active TSS	Duodenum Smooth Muscle	Duodenum
10	chr12:56550800-56553400	Active TSS	Fetal Intestine Large	intestine
11	chr12:56550800-56553600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr12:56551000-56553000	Active TSS	Brain Hippocampus Middle	brain
13	chr12:56551000-56553000	Active TSS	Brain Substantia Nigra	brain
14	chr12:56551000-56553200	Active TSS	H9 Cell Line	embryonic stem cell
15	chr12:56551000-56553200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr12:56551000-56553200	Active TSS	HUES64 Cell Line	embryonic stem cell
17	chr12:56551000-56553200	Active TSS	iPS-18 Cell Line	embryonic stem cell
18	chr12:56551000-56553200	Active TSS	Primary T cells from cord blood	blood
19	chr12:56551000-56553200	Active TSS	Colon Smooth Muscle	Colon
20	chr12:56551000-56553200	Active TSS	Esophagus	oesophagus
21	chr12:56551000-56553200	Active TSS	Left Ventricle	heart
22	chr12:56551000-56553400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr12:56551000-56553400	Active TSS	Aorta	Aorta
24	chr12:56551000-56553400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
25	chr12:56551000-56553400	Active TSS	Pancreas	Pancrea
26	chr12:56551000-56553600	Active TSS	Gastric	stomach
27	chr12:56551000-56554400	Active TSS	Ovary	ovary
28	chr12:56551200-56553200	Active TSS	H1 Cell Line	embryonic stem cell
29	chr12:56551200-56553400	Active TSS	Psoas Muscle	Psoas
30	chr12:56551200-56553400	Active TSS	Sigmoid Colon	Sigmoid Colon
31	chr12:56551200-56554200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr12:56551400-56553000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr12:56551400-56553000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr12:56551400-56553000	Active TSS	Breast Myoepithelial Primary Cells	Breast
35	chr12:56551400-56553000	Active TSS	Osteobl	bone
36	chr12:56551400-56553200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr12:56551400-56553200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr12:56551400-56553200	Active TSS	iPS-15b Cell Line	embryonic stem cell
39	chr12:56551400-56553200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr12:56551400-56553200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr12:56551400-56553200	Active TSS	Brain Cingulate Gyrus	brain
42	chr12:56551400-56553200	Active TSS	Duodenum Mucosa	Duodenum
43	chr12:56551400-56553200	Active TSS	Stomach Mucosa	stomach
44	chr12:56551400-56553200	Active TSS	Spleen	Spleen
45	chr12:56551400-56553400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr12:56551400-56553400	Active TSS	Lung	lung
47	chr12:56551400-56553400	Active TSS	Right Ventricle	heart
48	chr12:56551400-56553600	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr12:56551400-56553800	Active TSS	Right Atrium	heart
50	chr12:56551400-56554400	Active TSS	Small Intestine	intestine

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