Variant report

Variant	rs3812801
Chromosome Location	chr12:104235740-104235741
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	YY1	chr12:104235290-104235791	A549	lung:	n/a	n/a
2	SP1	chr12:104234837-104235793	H1-hESC	embryonic stem cell:	n/a	chr12:104235372-104235384 chr12:104235372-104235384 chr12:104235373-104235383
3	GTF2F1	chr12:104235561-104235771	H1-hESC	embryonic stem cell:	n/a	n/a
4	TCF12	chr12:104234709-104236111	A549	lung:	n/a	chr12:104235317-104235324 chr12:104235385-104235395
5	NR2F2	chr12:104235143-104236115	K562	blood:	n/a	n/a
6	SP1	chr12:104234838-104236128	A549	lung:	n/a	chr12:104235372-104235384 chr12:104235372-104235384 chr12:104235373-104235383
7	PBX3	chr12:104234828-104235924	A549	lung:	n/a	n/a
8	MAX	chr12:104234478-104236053	HepG2	liver:	n/a	chr12:104235191-104235200 chr12:104235040-104235050 chr12:104235041-104235050 chr12:104235041-104235051 chr12:104235042-104235051 chr12:104235373-104235383 chr12:104235042-104235049
9	MAX	chr12:104234611-104236055	Hela-S3	cervix:	n/a	chr12:104235191-104235200 chr12:104235040-104235050 chr12:104235041-104235050 chr12:104235041-104235051 chr12:104235042-104235051 chr12:104235373-104235383 chr12:104235042-104235049
10	RCOR1	chr12:104234603-104236081	K562	blood:	n/a	n/a
11	MAZ	chr12:104234555-104235963	HepG2	liver:	n/a	chr12:104235191-104235200 chr12:104235041-104235050 chr12:104235041-104235051 chr12:104235042-104235051 chr12:104235373-104235383 chr12:104235042-104235049
12	TCF12	chr12:104235167-104236267	MCF-7	breast:	n/a	chr12:104235317-104235324 chr12:104235385-104235395
13	MYC	chr12:104234347-104236046	MCF10A-Er-Src	breast:	n/a	chr12:104235191-104235200 chr12:104235040-104235050 chr12:104235041-104235050 chr12:104235041-104235051 chr12:104235042-104235051 chr12:104235373-104235383 chr12:104235042-104235049
14	HDAC2	chr12:104235541-104235887	K562	blood:	n/a	n/a
15	MAX	chr12:104234641-104235946	K562	blood:	n/a	chr12:104235191-104235200 chr12:104235040-104235050 chr12:104235041-104235050 chr12:104235041-104235051 chr12:104235042-104235051 chr12:104235373-104235383 chr12:104235042-104235049
16	MAX	chr12:104234421-104236110	NB4	blood:	n/a	chr12:104235191-104235200 chr12:104235040-104235050 chr12:104235041-104235050 chr12:104235041-104235051 chr12:104235042-104235051 chr12:104235373-104235383 chr12:104235042-104235049
17	TCF7L2	chr12:104235559-104236036	Hela-S3	cervix:	n/a	n/a
18	POLR2A	chr12:104235692-104235794	ProgFib	skin:	n/a	n/a
19	BHLHE40	chr12:104234855-104235930	K562	blood:	n/a	chr12:104235712-104235728 chr12:104235197-104235213 chr12:104234978-104234994
20	MYC	chr12:104234587-104236037	Hela-S3	cervix:	n/a	chr12:104235191-104235200 chr12:104235040-104235050 chr12:104235041-104235050 chr12:104235041-104235051 chr12:104235042-104235051 chr12:104235373-104235383 chr12:104235042-104235049
21	MAX	chr12:104234517-104236114	HCT-116	colon:	n/a	chr12:104235191-104235200 chr12:104235040-104235050 chr12:104235041-104235050 chr12:104235041-104235051 chr12:104235042-104235051 chr12:104235373-104235383 chr12:104235042-104235049
22	TAF1	chr12:104234341-104235800	H1-hESC	embryonic stem cell:	n/a	n/a
23	YY1	chr12:104235261-104235941	ECC-1	luminal epithelium:	n/a	n/a
24	POLR2A	chr12:104234743-104236126	K562	blood:	n/a	n/a
25	POLR2A	chr12:104234553-104236057	Hela-S3	cervix:	n/a	n/a
26	ESR1	chr12:104235539-104235931	ECC-1	luminal epithelium:	n/a	chr12:104235697-104235712
27	EGR1	chr12:104234211-104236032	HCT-116	colon:	n/a	chr12:104235534-104235549 chr12:104234375-104234389 chr12:104234376-104234387 chr12:104235113-104235127 chr12:104234376-104234387 chr12:104235150-104235164 chr12:104235536-104235547 chr12:104235230-104235239 chr12:104234371-104234393 chr12:104235720-104235734 chr12:104235133-104235147 chr12:104234377-104234387 chr12:104234375-104234388 chr12:104234376-104234390 chr12:104235085-104235099 chr12:104235227-104235240 chr12:104235227-104235240 chr12:104234377-104234387
28	EP300	chr12:104235713-104236085	SK-N-SH_RA	brain:	n/a	n/a
29	CHD2	chr12:104234598-104236048	Hela-S3	cervix:	n/a	n/a
30	POLR2A	chr12:104235552-104235856	H1-hESC	embryonic stem cell:	n/a	n/a
31	MYC	chr12:104235616-104235893	MCF-7	breast:	n/a	n/a
32	POLR2A	chr12:104234542-104236234	PFSK-1	brain:	n/a	n/a
33	POLR2A	chr12:104235606-104235779	HepG2	liver:	n/a	n/a
34	SIN3AK20	chr12:104234490-104235772	K562	blood:	n/a	n/a
35	CTCF	chr12:104235634-104235834	K562	blood:	n/a	chr12:104235676-104235689
36	POLR2A	chr12:104235639-104235811	A549	lung:	n/a	n/a
37	ESR1	chr12:104235532-104235921	T-47D	breast:	n/a	chr12:104235697-104235712
38	POLR2A	chr12:104234577-104235936	HepG2	liver:	n/a	n/a
39	TAF1	chr12:104235444-104235998	Hela-S3	cervix:	n/a	n/a
40	GATA3	chr12:104234670-104236118	A549	lung:	n/a	chr12:104235854-104235863 chr12:104235851-104235860
41	ELK4	chr12:104235555-104235948	Hela-S3	cervix:	n/a	n/a
42	E2F6	chr12:104235547-104235754	K562	blood:	n/a	n/a
43	MXI1	chr12:104235452-104236065	Hela-S3	cervix:	n/a	n/a
44	MAZ	chr12:104234528-104236014	Hela-S3	cervix:	n/a	chr12:104235191-104235200 chr12:104235041-104235050 chr12:104235041-104235051 chr12:104235042-104235051 chr12:104235373-104235383 chr12:104235042-104235049
45	RUNX3	chr12:104235138-104236160	GM12878	blood:	n/a	n/a
46	IRF1	chr12:104234634-104235860	K562	blood:	n/a	n/a
47	HEY1	chr12:104235156-104236047	K562	blood:	n/a	chr12:104235297-104235312
48	MXI1	chr12:104233534-104236201	SK-N-SH	brain:	n/a	n/a
49	EGR1	chr12:104234652-104235920	K562	blood:	n/a	chr12:104235534-104235549 chr12:104235113-104235127 chr12:104235150-104235164 chr12:104235536-104235547 chr12:104235230-104235239 chr12:104235720-104235734 chr12:104235133-104235147 chr12:104235085-104235099 chr12:104235227-104235240 chr12:104235227-104235240
50	BHLHE40	chr12:104235583-104235750	GM12878	blood:	n/a	chr12:104235712-104235728

No.	Distal block	Cell Line	Cell type
1	chr12:104156601..104158304-chr12:104234434..104236510,2	MCF-7	breast:
2	chr12:104192525..104200371-chr12:104233987..104238967,10	MCF-7	breast:
3	chr12:104234723..104236733-chr12:104679840..104682489,2	K562	blood:
4	chr12:104233909..104239694-chr12:104322835..104327398,8	K562	blood:
5	chr12:104160749..104162806-chr12:104234443..104236279,2	MCF-7	breast:
6	chr12:104211319..104217420-chr12:104233507..104236073,8	MCF-7	breast:
7	chr12:104234047..104236214-chr12:104531313..104532962,2	MCF-7	breast:
8	chr12:104233429..104235958-chr12:104358438..104361946,3	MCF-7	breast:
9	chr12:104234073..104236683-chr12:104349820..104352847,3	K562	blood:
10	chr12:104186877..104189949-chr12:104233437..104236104,3	MCF-7	breast:
11	chr1:28974871..28975747-chr12:104235261..104236177,2	Hela-S3	cervix:
12	chr12:104233800..104236223-chr12:104679514..104682489,2	K562	blood:
13	chr12:104208263..104213427-chr12:104233273..104236383,5	K562	blood:
14	chr12:104234122..104238773-chr12:104347839..104352988,5	MCF-7	breast:
15	chr12:104233713..104237034-chr12:104348727..104352026,4	MCF-7	breast:
16	chr12:56123120..56123867-chr12:104234782..104235765,2	Hela-S3	cervix:
17	chr12:104235342..104236842-chr12:104357860..104360492,2	K562	blood:
18	chr12:104233715..104236918-chr12:104321893..104325386,6	K562	blood:
19	chr12:104235292..104235920-chr7:26228161..26228786,2	Hela-S3	cervix:
20	chr12:104235142..104235987-chr6:86388387..86389071,2	Hela-S3	cervix:
21	chr12:104192326..104196273-chr12:104235179..104237558,3	K562	blood:
22	chr12:104235182..104235757-chr17:74067817..74068670,2	NB4	blood:

Variant related genes	Relation type
NT5DC3	TF binding region
ENSG00000120837	Chromatin interaction
ENSG00000166598	Chromatin interaction
ENSG00000257681	Chromatin interaction
ENSG00000265072	Chromatin interaction
ENSG00000257754	Chromatin interaction
ENSG00000204954	Chromatin interaction
ENSG00000136011	Chromatin interaction
ENSG00000167881	Chromatin interaction
ENSG00000214198	Chromatin interaction
ENSG00000135404	Chromatin interaction
ENSG00000270103	Chromatin interaction
ENSG00000198431	Chromatin interaction
ENSG00000203875	Chromatin interaction
ENSG00000139372	Chromatin interaction
ENSG00000111696	Chromatin interaction
ENSG00000186919	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10745984	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10778292	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10861130	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10861131	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10861142	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap]
rs10861143	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap]
rs10861146	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11111815	0.89[ASW][hapmap];0.91[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MKK][hapmap];0.92[YRI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11111821	0.86[EUR][1000 genomes]
rs11111831	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12302488	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12369947	0.83[CEU][hapmap]
rs12371102	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17034938	0.83[CEU][hapmap];0.92[MEX][hapmap]
rs2576969	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs4135138	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs6539103	0.95[ASN][1000 genomes]
rs7302036	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7968124	0.85[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs7971317	0.85[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs7971563	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9308316	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap]
rs9989004	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv34031	chr12:104114277-104298546	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
2	nsv560039	chr12:104177668-104455340	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
3	esv3372343	chr12:104234047-104236595	Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	34 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:104231800-104236000	Active TSS	Rectal Smooth Muscle	rectum
2	chr12:104232000-104236000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr12:104232400-104235800	Active TSS	Colon Smooth Muscle	Colon
4	chr12:104233000-104235800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr12:104233000-104236000	Active TSS	Duodenum Smooth Muscle	Duodenum
6	chr12:104233400-104236000	Active TSS	Fetal Brain Female	brain
7	chr12:104233600-104235800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr12:104233600-104236000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
9	chr12:104233600-104236000	Active TSS	Brain Substantia Nigra	brain
10	chr12:104233800-104235800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr12:104233800-104235800	Active TSS	Pancreatic Islets	Pancreatic Islet
12	chr12:104234000-104235800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr12:104234000-104235800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr12:104234000-104235800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr12:104234000-104235800	Active TSS	Esophagus	oesophagus
16	chr12:104234000-104235800	Active TSS	A549	lung
17	chr12:104234000-104235800	Active TSS	Hela-S3	cervix
18	chr12:104234000-104236000	Active TSS	ES-I3 Cell Line	embryonic stem cell
19	chr12:104234000-104236000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr12:104234000-104236000	Flanking Active TSS	Primary hematopoietic stem cells	blood
21	chr12:104234000-104236000	Active TSS	Colonic Mucosa	Colon
22	chr12:104234000-104236000	Active TSS	Fetal Kidney	kidney
23	chr12:104234200-104235800	Active TSS	Brain Angular Gyrus	brain
24	chr12:104234200-104235800	Active TSS	Brain Hippocampus Middle	brain
25	chr12:104234200-104235800	Active TSS	K562	blood
26	chr12:104234200-104236000	Active TSS	Brain Anterior Caudate	brain
27	chr12:104234200-104236000	Active TSS	Right Ventricle	heart
28	chr12:104234200-104236200	Active TSS	H9 Cell Line	embryonic stem cell
29	chr12:104234200-104236200	Active TSS	iPS-15b Cell Line	embryonic stem cell
30	chr12:104234200-104236200	Active TSS	Brain Cingulate Gyrus	brain
31	chr12:104234400-104236000	Active TSS	Psoas Muscle	Psoas
32	chr12:104234400-104236200	Active TSS	iPS-20b Cell Line	embryonic stem cell
33	chr12:104234600-104235800	Active TSS	HUES48 Cell Line	embryonic stem cell
34	chr12:104234600-104235800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr12:104234600-104235800	Active TSS	Brain Germinal Matrix	brain
36	chr12:104234600-104236000	Active TSS	Rectal Mucosa Donor 29	rectum
37	chr12:104234600-104236200	Active TSS	HUES64 Cell Line	embryonic stem cell
38	chr12:104234600-104236200	Active TSS	iPS-18 Cell Line	embryonic stem cell
39	chr12:104234600-104236200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr12:104234800-104235800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr12:104235200-104235800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
42	chr12:104235200-104235800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
43	chr12:104235200-104235800	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
44	chr12:104235200-104235800	Flanking Active TSS	Fetal Intestine Small	intestine
45	chr12:104235200-104235800	Flanking Active TSS	Fetal Muscle Leg	muscle
46	chr12:104235200-104236000	Flanking Active TSS	Primary B cells from cord blood	blood
47	chr12:104235200-104236000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
48	chr12:104235200-104236000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr12:104235200-104236000	Flanking Active TSS	Fetal Muscle Trunk	muscle
50	chr12:104235400-104235800	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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