Variant report

Variant	rs3838958
Chromosome Location	chr12:57521414-57521415
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	HEY1	chr12:57520762-57522457	HepG2	liver:	n/a	n/a
2	FOS	chr12:57521149-57521632	MCF10A-Er-Src	breast:	n/a	chr12:57521548-57521557 chr12:57521487-57521497 chr12:57521488-57521497 chr12:57521487-57521496
3	POLR2A	chr12:57520674-57522449	HepG2	liver:	n/a	n/a
4	ZBTB7A	chr12:57521052-57523126	ECC-1	luminal epithelium:	n/a	chr12:57522535-57522544 chr12:57523014-57523022 chr12:57522988-57522996
5	MAX	chr12:57520874-57522489	A549	lung:	n/a	chr12:57521653-57521663 chr12:57521582-57521591 chr12:57521685-57521695
6	SMARCB1	chr12:57520940-57522161	Hela-S3	cervix:	n/a	chr12:57521488-57521497 chr12:57521487-57521496
7	POLR2A	chr12:57521037-57522363	ECC-1	luminal epithelium:	n/a	n/a
8	E2F6	chr12:57521412-57521556	K562	blood:	n/a	n/a
9	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
10	JUND	chr12:57521049-57521666	HepG2	liver:	n/a	chr12:57521486-57521497 chr12:57521548-57521557 chr12:57521487-57521497 chr12:57521488-57521497 chr12:57521487-57521496
11	FOS	chr12:57521305-57521629	MCF10A-Er-Src	breast:	n/a	chr12:57521548-57521557 chr12:57521487-57521497 chr12:57521488-57521497 chr12:57521487-57521496
12	POLR2A	chr12:57521273-57522403	HUVEC	blood vessel:	n/a	n/a
13	POLR2A	chr12:57521148-57522227	MCF10A-Er-Src	breast:	n/a	n/a
14	HNF4G	chr12:57520983-57521908	HepG2	liver:	n/a	chr12:57521754-57521776 chr12:57521256-57521268 chr12:57521255-57521268 chr12:57521256-57521268 chr12:57521313-57521328
15	POLR2A	chr12:57521387-57521908	A549	lung:	n/a	n/a
16	CTCF	chr12:57520918-57521438	MCF-7	breast:	n/a	chr12:57521155-57521173 chr12:57521158-57521171
17	MAX	chr12:57520818-57522090	MCF-7	breast:	n/a	chr12:57521653-57521663 chr12:57521582-57521591 chr12:57521685-57521695
18	ZBTB7A	chr12:57521355-57522926	K562	blood:	n/a	chr12:57522535-57522544
19	CHD2	chr12:57521161-57521473	H1-hESC	embryonic stem cell:	n/a	n/a
20	YY1	chr12:57520921-57522129	HepG2	liver:	n/a	chr12:57521513-57521527 chr12:57521684-57521693
21	FOSL2	chr12:57521400-57521656	A549	lung:	n/a	chr12:57521548-57521557 chr12:57521487-57521497 chr12:57521488-57521497 chr12:57521487-57521496
22	CHD2	chr12:57521068-57521887	Hela-S3	cervix:	n/a	n/a
23	CTCF	chr12:57521360-57521510	HCPEpiC	choroid plexus:	n/a	n/a
24	TCF12	chr12:57520761-57522236	ECC-1	luminal epithelium:	n/a	n/a
25	MXI1	chr12:57520190-57524232	SK-N-SH	brain:	n/a	n/a
26	TAF1	chr12:57521401-57521832	HepG2	liver:	n/a	n/a
27	HNF4G	chr12:57520929-57521587	HepG2	liver:	n/a	chr12:57521256-57521268 chr12:57521255-57521268 chr12:57521256-57521268 chr12:57521313-57521328
28	EP300	chr12:57520972-57521439	HepG2	liver:	n/a	n/a
29	JUND	chr12:57521187-57521656	HepG2	liver:	n/a	chr12:57521486-57521497 chr12:57521548-57521557 chr12:57521487-57521497 chr12:57521488-57521497 chr12:57521487-57521496
30	MYBL2	chr12:57520812-57522104	HepG2	liver:	n/a	n/a
31	FOSL2	chr12:57520978-57521728	HepG2	liver:	n/a	chr12:57521548-57521557 chr12:57521487-57521497 chr12:57521488-57521497 chr12:57521487-57521496
32	TCF12	chr12:57520906-57522366	A549	lung:	n/a	n/a
33	REST	chr12:57521012-57521589	HepG2	liver:	n/a	n/a
34	POLR2A	chr12:57521128-57522308	MCF-7	breast:	n/a	n/a
35	TAF1	chr12:57520731-57522332	ECC-1	luminal epithelium:	n/a	n/a
36	JUND	chr12:57521151-57521924	MCF-7	breast:	n/a	chr12:57521486-57521497 chr12:57521548-57521557 chr12:57521487-57521497 chr12:57521488-57521497 chr12:57521487-57521496
37	POLR2A	chr12:57520745-57524477	U87	brain:	n/a	n/a
38	CEBPD	chr12:57521067-57522492	HepG2	liver:	n/a	n/a
39	E2F6	chr12:57520859-57521449	A549	lung:	n/a	n/a
40	POLR2A	chr12:57520913-57522456	HCT-116	colon:	n/a	n/a
41	MAX	chr12:57520746-57522367	ECC-1	luminal epithelium:	n/a	chr12:57521653-57521663 chr12:57521582-57521591 chr12:57521685-57521695
42	POLR2A	chr12:57520955-57522425	HCT-116	colon:	n/a	n/a
43	EGR1	chr12:57521378-57522193	K562	blood:	n/a	chr12:57521684-57521699 chr12:57521685-57521698 chr12:57521686-57521696 chr12:57521653-57521663 chr12:57521650-57521663 chr12:57521544-57521554 chr12:57521646-57521668 chr12:57522132-57522141
44	POLR2A	chr12:57521404-57522199	HepG2	liver:	n/a	n/a
45	CTCF	chr12:57521300-57521450	HCPEpiC	choroid plexus:	n/a	n/a
46	HNF4A	chr12:57520962-57521974	HepG2	liver:	n/a	chr12:57521754-57521776 chr12:57521256-57521268 chr12:57521255-57521268 chr12:57521254-57521269 chr12:57521256-57521268 chr12:57521313-57521328
47	MAX	chr12:57520781-57522270	HepG2	liver:	n/a	chr12:57521653-57521663 chr12:57521582-57521591 chr12:57521685-57521695
48	JUND	chr12:57521037-57522207	K562	blood:	n/a	chr12:57521486-57521497 chr12:57521548-57521557 chr12:57521487-57521497 chr12:57521488-57521497 chr12:57521487-57521496
49	MXI1	chr12:57520727-57522972	IMR90	lung:	n/a	n/a
50	NR2F2	chr12:57520690-57521519	K562	blood:	n/a	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	chr12:57521248..57521856-chr6:32861681..32862282,2	Hela-S3	cervix:
5	chr12:57502755..57504582-chr12:57519285..57521755,2	K562	blood:
6	chr12:57478321..57481410-chr12:57519789..57521729,3	MCF-7	breast:
7	chr12:57482277..57484373-chr12:57520375..57523117,3	MCF-7	breast:
8	chr12:57521101..57521715-chr12:57636313..57637063,2	MCF-7	breast:
9	chr12:57490642..57492474-chr12:57520251..57522738,2	MCF-7	breast:
10	chr11:62608513..62609452-chr12:57521124..57522003,2	Hela-S3	cervix:
11	chr12:57513705..57517929-chr12:57519571..57523661,4	K562	blood:
12	chr12:57520657..57521652-chr12:57632774..57633462,3	K562	blood:
13	chr12:57520642..57521644-chr12:57576487..57577362,6	MCF-7	breast:
14	chr12:57520290..57524994-chr12:57525334..57528665,7	K562	blood:
15	chr12:57479977..57484073-chr12:57519609..57523791,10	MCF-7	breast:
16	chr12:57462031..57464946-chr12:57520259..57521909,2	MCF-7	breast:
17	chr12:57521132..57523355-chr12:57632415..57635225,2	K562	blood:
18	chr12:57520220..57523882-chr12:57558135..57563846,11	MCF-7	breast:
19	chr12:57503926..57506470-chr12:57520172..57522484,3	MCF-7	breast:
20	chr12:57520108..57523293-chr12:57525745..57528597,4	MCF-7	breast:
21	chr12:57520960..57521610-chr12:57569821..57570544,2	MCF-7	breast:
22	chr12:57520113..57524524-chr12:57557752..57564598,9	MCF-7	breast:
23	chr12:57520295..57521910-chr12:57627423..57630374,2	K562	blood:
24	chr11:65274183..65274686-chr12:57521118..57521989,2	Hela-S3	cervix:
25	chr12:57398801..57400743-chr12:57521280..57524489,3	K562	blood:
26	chr12:57520730..57521608-chr12:57566533..57567411,3	MCF-7	breast:
27	chr12:57520750..57521474-chr12:57560771..57561326,2	MCF-7	breast:
28	chr12:57501699..57504255-chr12:57519285..57521446,2	K562	blood:
29	chr12:57520628..57522201-chr12:57566487..57567403,12	MCF-7	breast:
30	chr12:57503796..57506425-chr12:57518057..57521814,4	MCF-7	breast:
31	chr12:57520979..57521583-chr12:57576381..57577009,2	MCF-7	breast:

Variant related genes	Relation type
LRP1	TF binding region
ENSG00000123384	Chromatin interaction
ENSG00000196531	Chromatin interaction
ENSG00000166881	Chromatin interaction
ENSG00000185633	Chromatin interaction
ENSG00000263832	Chromatin interaction
ENSG00000133316	Chromatin interaction
ENSG00000166886	Chromatin interaction
ENSG00000166888	Chromatin interaction
ENSG00000166860	Chromatin interaction
ENSG00000259125	Chromatin interaction

Extended variants
information (count: 5 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs12368672	0.83[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs73120411	0.84[AFR][1000 genomes];0.90[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	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:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:57505800-57521800	Weak transcription	Spleen	Spleen
2	chr12:57520400-57522200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr12:57520400-57524800	Active TSS	Rectal Smooth Muscle	rectum
4	chr12:57520600-57521600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
5	chr12:57520600-57521800	Enhancers	Fetal Brain Male	brain
6	chr12:57520600-57523600	Active TSS	HUES64 Cell Line	embryonic stem cell
7	chr12:57520600-57523600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr12:57520800-57521600	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
9	chr12:57520800-57521600	Flanking Active TSS	Osteobl	bone
10	chr12:57520800-57522200	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
11	chr12:57520800-57523200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr12:57520800-57523600	Active TSS	ES-I3 Cell Line	embryonic stem cell
13	chr12:57520800-57523600	Active TSS	H9 Cell Line	embryonic stem cell
14	chr12:57520800-57523800	Active TSS	Brain Hippocampus Middle	brain
15	chr12:57520800-57524000	Active TSS	HUES48 Cell Line	embryonic stem cell
16	chr12:57520800-57524000	Active TSS	Fetal Kidney	kidney
17	chr12:57520800-57524800	Active TSS	Right Atrium	heart
18	chr12:57521000-57521600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
19	chr12:57521000-57521600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
20	chr12:57521000-57521600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr12:57521000-57521600	Flanking Bivalent TSS/Enh	Thymus	Thymus
22	chr12:57521000-57522000	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
23	chr12:57521000-57522000	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
24	chr12:57521000-57522200	Flanking Bivalent TSS/Enh	Primary Natural Killer cells fromperipheralblood	blood
25	chr12:57521000-57522600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr12:57521000-57522600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr12:57521000-57522600	Active TSS	Fetal Brain Female	brain
28	chr12:57521000-57523400	Active TSS	Aorta	Aorta
29	chr12:57521000-57523400	Active TSS	Pancreatic Islets	Pancreatic Islet
30	chr12:57521000-57523600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr12:57521000-57523600	Active TSS	Pancreas	Pancrea
32	chr12:57521000-57523800	Active TSS	iPS-20b Cell Line	embryonic stem cell
33	chr12:57521000-57523800	Active TSS	Lung	lung
34	chr12:57521000-57525000	Active TSS	Psoas Muscle	Psoas
35	chr12:57521200-57521600	Flanking Bivalent TSS/Enh	Primary B cells from cord blood	blood
36	chr12:57521200-57521600	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
37	chr12:57521200-57521600	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
38	chr12:57521200-57521600	Flanking Active TSS	Placenta	Placenta
39	chr12:57521200-57521600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
40	chr12:57521200-57521800	Active TSS	Liver	Liver
41	chr12:57521200-57521800	Weak transcription	Fetal Heart	heart
42	chr12:57521200-57522000	Flanking Active TSS	Primary B cells from peripheral blood	blood
43	chr12:57521200-57522200	Flanking Active TSS	Primary hematopoietic stem cells	blood
44	chr12:57521200-57522200	Flanking Bivalent TSS/Enh	Dnd41	blood
45	chr12:57521200-57522200	Flanking Active TSS	HMEC	breast
46	chr12:57521200-57522600	Bivalent/Poised TSS	Primary T cells from cord blood	blood
47	chr12:57521200-57522600	Active TSS	A549	lung
48	chr12:57521200-57522600	Active TSS	Hela-S3	cervix
49	chr12:57521200-57523200	Active TSS	Breast Myoepithelial Primary Cells	Breast
50	chr12:57521200-57523400	Active TSS	H1 Cell Line	embryonic stem cell

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