Variant report

Variant	rs34890469
Chromosome Location	chr12:57521173-57521174
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	CTCF	chr12:57521040-57521190	HL-60	blood:	n/a	chr12:57521155-57521173 chr12:57521158-57521171
2	CTCF	chr12:57521060-57521210	GM12873	blood:	n/a	chr12:57521155-57521173 chr12:57521158-57521171
3	HEY1	chr12:57520762-57522457	HepG2	liver:	n/a	n/a
4	FOS	chr12:57521149-57521632	MCF10A-Er-Src	breast:	n/a	chr12:57521548-57521557 chr12:57521487-57521497 chr12:57521488-57521497 chr12:57521487-57521496
5	POLR2A	chr12:57520674-57522449	HepG2	liver:	n/a	n/a
6	RAD21	chr12:57521014-57521254	H1-hESC	embryonic stem cell:	n/a	chr12:57521161-57521173 chr12:57521156-57521175
7	CTCF	chr12:57521100-57521250	GM12872	blood:	n/a	chr12:57521155-57521173 chr12:57521158-57521171
8	USF2	chr12:57520942-57521261	Hela-S3	cervix:	n/a	n/a
9	ZBTB7A	chr12:57521052-57523126	ECC-1	luminal epithelium:	n/a	chr12:57522535-57522544 chr12:57523014-57523022 chr12:57522988-57522996
10	MAX	chr12:57520874-57522489	A549	lung:	n/a	chr12:57521653-57521663 chr12:57521582-57521591 chr12:57521685-57521695
11	SMARCB1	chr12:57520940-57522161	Hela-S3	cervix:	n/a	chr12:57521488-57521497 chr12:57521487-57521496
12	MAFK	chr12:57521173-57521223	HepG2	liver:	n/a	n/a
13	ZNF143	chr12:57521110-57521334	GM12878	blood:	n/a	n/a
14	POLR2A	chr12:57521037-57522363	ECC-1	luminal epithelium:	n/a	n/a
15	JUND	chr12:57521082-57521898	H1-hESC	embryonic stem cell:	n/a	chr12:57521486-57521497 chr12:57521548-57521557 chr12:57521487-57521497 chr12:57521488-57521497 chr12:57521487-57521496
16	CTCF	chr12:57521060-57521210	WERI-Rb-1	eye:	n/a	chr12:57521155-57521173 chr12:57521158-57521171
17	JUND	chr12:57521049-57521666	HepG2	liver:	n/a	chr12:57521486-57521497 chr12:57521548-57521557 chr12:57521487-57521497 chr12:57521488-57521497 chr12:57521487-57521496
18	FOXA2	chr12:57520975-57521260	HepG2	liver:	n/a	n/a
19	CTCF	chr12:57521060-57521210	HRE	kidney:	n/a	chr12:57521155-57521173 chr12:57521158-57521171
20	CTCF	chr12:57521046-57521234	SK-N-SH_RA	brain:	n/a	chr12:57521155-57521173 chr12:57521158-57521171
21	CTCF	chr12:57521087-57521234	Lung_OC	lung:	n/a	chr12:57521155-57521173 chr12:57521158-57521171
22	CTCF	chr12:57521120-57521270	GM06990	blood:	n/a	chr12:57521155-57521173 chr12:57521158-57521171
23	CTCF	chr12:57521062-57521278	K562	blood:	n/a	chr12:57521155-57521173 chr12:57521158-57521171
24	POLR2A	chr12:57521148-57522227	MCF10A-Er-Src	breast:	n/a	n/a
25	HNF4G	chr12:57520983-57521908	HepG2	liver:	n/a	chr12:57521754-57521776 chr12:57521256-57521268 chr12:57521255-57521268 chr12:57521256-57521268 chr12:57521313-57521328
26	CTCF	chr12:57520918-57521438	MCF-7	breast:	n/a	chr12:57521155-57521173 chr12:57521158-57521171
27	POLR2A	chr12:57521129-57521360	HepG2	liver:	n/a	n/a
28	GTF2F1	chr12:57521072-57521290	H1-hESC	embryonic stem cell:	n/a	n/a
29	MAX	chr12:57520818-57522090	MCF-7	breast:	n/a	chr12:57521653-57521663 chr12:57521582-57521591 chr12:57521685-57521695
30	CTCF	chr12:57521084-57521282	LNCaP	prostate:	n/a	chr12:57521155-57521173 chr12:57521158-57521171
31	RAD21	chr12:57520917-57521395	A549	lung:	n/a	chr12:57521161-57521173 chr12:57521156-57521175
32	BRCA1	chr12:57521134-57521284	HepG2	liver:	n/a	n/a
33	CHD2	chr12:57521161-57521473	H1-hESC	embryonic stem cell:	n/a	n/a
34	TAF1	chr12:57521081-57521346	HepG2	liver:	n/a	n/a
35	YY1	chr12:57520921-57522129	HepG2	liver:	n/a	chr12:57521513-57521527 chr12:57521684-57521693
36	CTCF	chr12:57521080-57521230	BE2_C	brain:	n/a	chr12:57521155-57521173 chr12:57521158-57521171
37	YY1	chr12:57520997-57521398	K562	blood:	n/a	n/a
38	CTCF	chr12:57521080-57521230	HCT-116	colon:	n/a	chr12:57521155-57521173 chr12:57521158-57521171
39	CTCF	chr12:57521060-57521210	HFF	foreskin:	n/a	chr12:57521155-57521173 chr12:57521158-57521171
40	CTCF	chr12:57520994-57521339	GM12878	blood:	n/a	chr12:57521155-57521173 chr12:57521158-57521171
41	SMC3	chr12:57521089-57521320	GM12878	blood:	n/a	chr12:57521157-57521171
42	EP300	chr12:57521016-57521287	K562	blood:	n/a	n/a
43	CTCF	chr12:57521140-57521290	AG04449	skin:	n/a	chr12:57521155-57521173 chr12:57521158-57521171
44	CREB1	chr12:57520995-57521354	A549	lung:	n/a	n/a
45	CTCF	chr12:57521060-57521210	HAc	cerebellar:	n/a	chr12:57521155-57521173 chr12:57521158-57521171
46	CTCF	chr12:57521060-57521210	HCT-116	colon:	n/a	chr12:57521155-57521173 chr12:57521158-57521171
47	TCF7L2	chr12:57520954-57521401	Hela-S3	cervix:	n/a	n/a
48	CHD2	chr12:57521068-57521887	Hela-S3	cervix:	n/a	n/a
49	ARID3A	chr12:57521081-57521273	HepG2	liver:	n/a	n/a
50	CTCF	chr12:57521060-57521210	NHLF	lung:	n/a	chr12:57521155-57521173 chr12:57521158-57521171

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr12:57521155-57521205	Hela-S3	cervix:	n/a
2	chr12:57521155-57521205	HL-60	blood:	n/a
3	chr12:57521155-57521205	HRCEpiC	kidney:	n/a
4	chr12:57521155-57521205	AG09309	skin:	n/a
5	chr12:57521155-57521205	AG04450	lung:	fetal
6	chr12:57521155-57521205	BJ	skin:	n/a
7	chr12:57521155-57521205	HAEpiC	amniotic membrane:	n/a
8	chr12:57521155-57521205	IMR90	lung:	fetal
9	chr12:57521155-57521205	NHDF-neo	bronchial:	n/a
10	chr12:57521155-57521205	NHBE	bronchial:	n/a
11	chr12:57521155-57521205	K562	blood:	n/a
12	chr12:57521155-57521205	SK-N-MC	brain:	n/a
13	chr12:57521155-57521205	ECC-1	luminal epithelium:	n/a
14	chr12:57521155-57521205	HUVEC	blood vessel:	n/a
15	chr12:57521155-57521205	NB4	blood:	n/a
16	chr12:57521155-57521205	ovcar-3	ovarian:	n/a
17	chr12:57521155-57521205	SAEC	small airway:	n/a
18	chr12:57521155-57521205	GM06990	blood:	n/a
19	chr12:57521155-57521205	AoSMC	blood vessel:	n/a
20	chr12:57521155-57521205	NH-A	brain:	n/a
21	chr12:57521155-57521205	T-47D	breast:	n/a
22	chr12:57521155-57521205	HCM	heart:	n/a
23	chr12:57521155-57521205	SKMC	muscle:	n/a
24	chr12:57521155-57521205	HNPCEpiC	eye:	n/a
25	chr12:57521155-57521205	HepG2	liver:	n/a
26	chr12:57521155-57521205	HRE	kidney:	n/a
27	chr12:57521155-57521205	SK-N-SH_RA	brain:	n/a
28	chr12:57521155-57521205	BE2_C	brain:	n/a
29	chr12:57521155-57521205	GM19239	blood:	n/a
30	chr12:57521155-57521205	U87	brain:	n/a
31	chr12:57521155-57521205	RPTEC	kidney:	n/a
32	chr12:57521155-57521205	ProgFib	skin:	n/a
33	chr12:57521155-57521205	H1-hESC	embryonic stem cell:	embryo
34	chr12:57521155-57521205	PrEC	prostate:	n/a
35	chr12:57521155-57521205	SK-N-SH	brain:	n/a
36	chr12:57521155-57521205	HCF	heart:	n/a
37	chr12:57521155-57521205	HIPEpiC	eye:	n/a
38	chr12:57521155-57521205	Hepatocyte	liver:	n/a
39	chr12:57521155-57521205	PANC-1	pancreas:	n/a
40	chr12:57521155-57521205	A549	lung:	n/a
41	chr12:57521155-57521205	Jurkat	blood:	n/a
42	chr12:57521155-57521205	GM12878	blood:	n/a
43	chr12:57521155-57521205	GM12891	blood:	n/a
44	chr12:57521155-57521205	HPAEpiC	pulmonary alveolar:	n/a
45	chr12:57521155-57521205	CMK	blood:	n/a
46	chr12:57521155-57521205	HRPEpiC	eye:	n/a
47	chr12:57521155-57521205	MCF-7	breast:	n/a
48	chr12:57521155-57521205	HEK293	kidney:	embryo
49	chr12:57521155-57521205	HMEC	breast:	n/a
50	chr12:57521155-57521205	HCPEpiC	choroid plexus:	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:57520592..57523929-chr12:57539571..57544778,8	MCF-7	breast:
2	chr12:57117761..57120217-chr12:57520609..57523242,3	K562	blood:
3	chr12:57504588..57507979-chr12:57520002..57522760,4	K562	blood:
4	chr12:57502755..57504582-chr12:57519285..57521755,2	K562	blood:
5	chr12:57478321..57481410-chr12:57519789..57521729,3	MCF-7	breast:
6	chr12:57482277..57484373-chr12:57520375..57523117,3	MCF-7	breast:
7	chr12:57521101..57521715-chr12:57636313..57637063,2	MCF-7	breast:
8	chr12:57490642..57492474-chr12:57520251..57522738,2	MCF-7	breast:
9	chr11:62608513..62609452-chr12:57521124..57522003,2	Hela-S3	cervix:
10	chr12:57513705..57517929-chr12:57519571..57523661,4	K562	blood:
11	chr12:57520657..57521652-chr12:57632774..57633462,3	K562	blood:
12	chr12:57520642..57521644-chr12:57576487..57577362,6	MCF-7	breast:
13	chr12:57520290..57524994-chr12:57525334..57528665,7	K562	blood:
14	chr12:57479977..57484073-chr12:57519609..57523791,10	MCF-7	breast:
15	chr12:57462031..57464946-chr12:57520259..57521909,2	MCF-7	breast:
16	chr12:57521132..57523355-chr12:57632415..57635225,2	K562	blood:
17	chr12:57520220..57523882-chr12:57558135..57563846,11	MCF-7	breast:
18	chr12:57503926..57506470-chr12:57520172..57522484,3	MCF-7	breast:
19	chr12:57520108..57523293-chr12:57525745..57528597,4	MCF-7	breast:
20	chr12:57520960..57521610-chr12:57569821..57570544,2	MCF-7	breast:
21	chr12:57520113..57524524-chr12:57557752..57564598,9	MCF-7	breast:
22	chr12:57520295..57521910-chr12:57627423..57630374,2	K562	blood:
23	chr11:65274183..65274686-chr12:57521118..57521989,2	Hela-S3	cervix:
24	chr12:57480206..57483796-chr12:57518313..57521204,3	K562	blood:
25	chr12:57520730..57521608-chr12:57566533..57567411,3	MCF-7	breast:
26	chr12:57520750..57521474-chr12:57560771..57561326,2	MCF-7	breast:
27	chr12:57501699..57504255-chr12:57519285..57521446,2	K562	blood:
28	chr12:57520628..57522201-chr12:57566487..57567403,12	MCF-7	breast:
29	chr12:57503796..57506425-chr12:57518057..57521814,4	MCF-7	breast:
30	chr12:57520979..57521583-chr12:57576381..57577009,2	MCF-7	breast:

Variant related genes	Relation type
LRP1	TF binding region
LRP1	CpG island
ENSG00000259125	Chromatin interaction
ENSG00000185633	Chromatin interaction
ENSG00000166881	Chromatin interaction
ENSG00000133316	Chromatin interaction
ENSG00000196531	Chromatin interaction
ENSG00000123384	Chromatin interaction
ENSG00000263832	Chromatin interaction
ENSG00000166888	Chromatin interaction
ENSG00000166886	Chromatin interaction

Extended variants
information (count: 7 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs59902070	1.00[AFR][1000 genomes]
rs61626321	1.00[AFR][1000 genomes]
rs73338525	0.91[AFR][1000 genomes]
rs73340505	0.91[AFR][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	nsv1040850	chr12:57055011-57679209	Strong transcription Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	181 gene(s)	inside rSNPs	diseases
2	nsv428590	chr12:57329214-57527358	Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
3	nsv832428	chr12:57340609-57535694	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:57505800-57521800	Weak transcription	Spleen	Spleen
2	chr12:57520400-57521200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr12:57520400-57521200	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
4	chr12:57520400-57521200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr12:57520400-57521200	Flanking Active TSS	Liver	Liver
6	chr12:57520400-57521200	Enhancers	Esophagus	oesophagus
7	chr12:57520400-57521200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
8	chr12:57520400-57521200	Flanking Active TSS	Hela-S3	cervix
9	chr12:57520400-57521200	Flanking Active TSS	HepG2	liver
10	chr12:57520400-57521200	Enhancers	HMEC	breast
11	chr12:57520400-57521400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr12:57520400-57521400	Flanking Active TSS	Duodenum Mucosa	Duodenum
13	chr12:57520400-57521400	Enhancers	Small Intestine	intestine
14	chr12:57520400-57522200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr12:57520400-57524800	Active TSS	Rectal Smooth Muscle	rectum
16	chr12:57520600-57521200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr12:57520600-57521200	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr12:57520600-57521200	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
19	chr12:57520600-57521200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr12:57520600-57521200	Flanking Active TSS	Fetal Intestine Small	intestine
21	chr12:57520600-57521200	Flanking Active TSS	Stomach Mucosa	stomach
22	chr12:57520600-57521200	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
23	chr12:57520600-57521400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr12:57520600-57521400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr12:57520600-57521400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
26	chr12:57520600-57521400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr12:57520600-57521400	Flanking Active TSS	Adipose Nuclei	Adipose
28	chr12:57520600-57521400	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
29	chr12:57520600-57521400	Bivalent Enhancer	Fetal Thymus	thymus
30	chr12:57520600-57521400	Flanking Active TSS	Stomach Smooth Muscle	stomach
31	chr12:57520600-57521400	Flanking Active TSS	K562	blood
32	chr12:57520600-57521600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
33	chr12:57520600-57521800	Enhancers	Fetal Brain Male	brain
34	chr12:57520600-57523600	Active TSS	HUES64 Cell Line	embryonic stem cell
35	chr12:57520600-57523600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr12:57520800-57521200	Flanking Active TSS	H1 Cell Line	embryonic stem cell
37	chr12:57520800-57521200	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr12:57520800-57521200	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
39	chr12:57520800-57521200	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
40	chr12:57520800-57521200	Enhancers	Primary T helper naive cells from peripheral blood	blood
41	chr12:57520800-57521200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
42	chr12:57520800-57521200	Flanking Active TSS	Brain Angular Gyrus	brain
43	chr12:57520800-57521200	Flanking Active TSS	Brain Anterior Caudate	brain
44	chr12:57520800-57521200	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
45	chr12:57520800-57521200	Flanking Active TSS	Colonic Mucosa	Colon
46	chr12:57520800-57521200	Flanking Active TSS	Fetal Intestine Large	intestine
47	chr12:57520800-57521200	Enhancers	Placenta	Placenta
48	chr12:57520800-57521200	Flanking Active TSS	Gastric	stomach
49	chr12:57520800-57521200	Flanking Active TSS	Left Ventricle	heart
50	chr12:57520800-57521200	Flanking Active TSS	Placenta Amnion	Placenta Amnion

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