Variant report

Variant	rs3825096
Chromosome Location	chr12:122884076-122884077
allele	C/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	chr12:122883876-122885661	U87	brain:	n/a	n/a
2	RAD21	chr12:122883906-122884467	ECC-1	luminal epithelium:	n/a	n/a
3	CTCF	chr12:122884005-122884375	K562	blood:	n/a	n/a
4	JUND	chr12:122883910-122885548	HCT-116	colon:	n/a	chr12:122885189-122885199 chr12:122885189-122885198 chr12:122885190-122885199 chr12:122885188-122885199 chr12:122885188-122885200 chr12:122885190-122885197 chr12:122885191-122885202
5	RCOR1	chr12:122883896-122885627	Hela-S3	cervix:	n/a	n/a
6	GATA3	chr12:122883671-122884627	SK-N-SH	brain:	n/a	chr12:122883982-122883994 chr12:122883980-122883996 chr12:122883982-122883989
7	TBL1XR1	chr12:122884014-122884679	K562	blood:	n/a	n/a
8	TCF12	chr12:122883841-122886012	A549	lung:	n/a	chr12:122885321-122885330
9	CTCF	chr12:122884060-122884210	GM12866	blood:	n/a	n/a
10	STAT5A	chr12:122884010-122884768	GM12878	blood:	n/a	n/a
11	CBX3	chr12:122883983-122885366	K562	blood:	n/a	n/a
12	CTCF	chr12:122883978-122884422	GM12878	blood:	n/a	n/a
13	USF1	chr12:122884045-122884385	A549	lung:	n/a	n/a
14	SMC3	chr12:122883915-122884473	K562	blood:	n/a	n/a
15	GATA2	chr12:122883624-122884635	HUVEC	blood vessel:	n/a	chr12:122883982-122883994 chr12:122883980-122883996 chr12:122883982-122883989 chr12:122883982-122883996
16	EP300	chr12:122883991-122885340	K562	blood:	n/a	chr12:122885190-122885199
17	CTCF	chr12:122884057-122884358	GM12878	blood:	n/a	n/a
18	MTA3	chr12:122883900-122885461	GM12878	blood:	n/a	n/a
19	TEAD4	chr12:122883982-122884398	H1-hESC	embryonic stem cell:	n/a	n/a
20	TBP	chr12:122884071-122885353	HepG2	liver:	n/a	n/a
21	CTCF	chr12:122884060-122884210	HFF	foreskin:	n/a	n/a
22	RAD21	chr12:122883766-122885514	HCT-116	colon:	n/a	n/a
23	CTCF	chr12:122884011-122884426	H1-hESC	embryonic stem cell:	n/a	n/a
24	FOXM1	chr12:122883820-122884603	GM12878	blood:	n/a	n/a
25	CREB1	chr12:122884019-122884760	GM12878	blood:	n/a	n/a
26	IRF1	chr12:122883715-122885366	K562	blood:	n/a	chr12:122883900-122883914 chr12:122883900-122883910 chr12:122884607-122884621 chr12:122884101-122884114 chr12:122885136-122885145
27	RAD21	chr12:122883445-122885347	SK-N-SH	brain:	n/a	n/a
28	POLR2A	chr12:122883907-122884870	K562	blood:	n/a	n/a
29	CREB1	chr12:122883967-122884902	HepG2	liver:	n/a	n/a
30	CEBPB	chr12:122884039-122884858	A549	lung:	n/a	chr12:122884690-122884702
31	EP300	chr12:122884059-122885387	GM12878	blood:	n/a	chr12:122885190-122885199 chr12:122885347-122885361
32	MAX	chr12:122883981-122885530	HepG2	liver:	n/a	n/a
33	SIX5	chr12:122883696-122885577	A549	lung:	n/a	n/a
34	MYBL2	chr12:122883859-122885606	HepG2	liver:	n/a	n/a
35	POLR2A	chr12:122883916-122885418	PANC-1	pancreas:	n/a	n/a
36	GATA1	chr12:122883791-122884613	PBDE	blood:	n/a	chr12:122883982-122883994 chr12:122883980-122883996 chr12:122883982-122883989
37	EP300	chr12:122884012-122885493	ECC-1	luminal epithelium:	n/a	chr12:122885190-122885199 chr12:122885347-122885361
38	RAD21	chr12:122884016-122884613	A549	lung:	n/a	n/a
39	RAD21	chr12:122883802-122885389	Hela-S3	cervix:	n/a	n/a
40	MAFF	chr12:122884068-122885402	HepG2	liver:	n/a	n/a
41	CEBPB	chr12:122884073-122884765	GM12878	blood:	n/a	chr12:122884690-122884702
42	RFX5	chr12:122883975-122885398	Hela-S3	cervix:	n/a	n/a
43	MAX	chr12:122883892-122884737	K562	blood:	n/a	n/a
44	CEBPB	chr12:122883982-122885534	A549	lung:	n/a	chr12:122885349-122885362 chr12:122884690-122884702 chr12:122885349-122885360 chr12:122885349-122885360
45	POLR2A	chr12:122883655-122885522	PANC-1	pancreas:	n/a	n/a
46	CTCF	chr12:122884059-122884344	Medullo	brain:	n/a	n/a
47	MAX	chr12:122884063-122885424	Hela-S3	cervix:	n/a	n/a
48	CTCF	chr12:122884017-122884359	Spleen_OC	spleen:	n/a	n/a
49	SMC3	chr12:122883756-122885397	Hela-S3	cervix:	n/a	n/a
50	GATA3	chr12:122883688-122884773	T-47D	breast:	n/a	chr12:122883982-122883994 chr12:122883980-122883996 chr12:122883982-122883989

No.	Distal block	Cell Line	Cell type
1	chr12:122882610..122885113-chr12:122985473..122987082,2	K562	blood:
2	chr12:122883532..122886049-chr12:123009837..123012984,6	K562	blood:
3	chr12:122882568..122884696-chr12:122981168..122984063,2	K562	blood:
4	chr12:122883132..122886264-chr12:123235650..123239708,3	MCF-7	breast:
5	chr12:122883776..122884551-chr12:122906694..122907223,2	K562	blood:
6	chr12:122878851..122886809-chr12:122904517..122908613,16	MCF-7	breast:
7	chr12:122879571..122888507-chr12:122899670..122909196,27	K562	blood:
8	chr12:122880014..122886193-chr12:123009799..123012848,10	K562	blood:
9	chr12:122882673..122885520-chr12:122982556..122985171,3	K562	blood:
10	chr12:122883071..122886014-chr6:33242178..33244499,2	K562	blood:
11	chr12:122882637..122886040-chr12:123010001..123012682,3	MCF-7	breast:
12	chr12:122877588..122886723-chr12:122904086..122910536,22	K562	blood:
13	chr12:122879653..122881712-chr12:122883701..122886016,2	MCF-7	breast:
14	chr12:122883813..122884476-chr12:122906517..122907101,2	MCF-7	breast:
15	chr12:122883163..122885704-chr12:123007231..123009242,2	K562	blood:
16	chr12:122882564..122887396-chr12:122904302..122908331,13	MCF-7	breast:
17	chr12:122883160..122884972-chr12:122965630..122967468,3	K562	blood:
18	chr12:122864255..122866125-chr12:122882192..122884983,2	K562	blood:
19	chr12:122883747..122886226-chr12:122990719..122993167,2	K562	blood:
20	chr12:122883399..122884323-chr12:122906252..122907251,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-KNTC1-1	chr12:122883843-122885404	ENSG00000257097
2	lnc-KNTC1-1	chr12:122883843-122884165	ENSG00000257097
3	lnc-KNTC1-1	chr12:122883843-122884441	NONHSAT031506
4	lnc-KNTC1-1	chr12:122883843-122884491	NR_045382

Variant related genes	Relation type
CLIP1	TF binding region
ENSG00000033030	Chromatin interaction
ENSG00000139726	Chromatin interaction
ENSG00000184445	Chromatin interaction
ENSG00000257097	Chromatin interaction
ENSG00000231500	Chromatin interaction
ENSG00000130779	Chromatin interaction
ENSG00000111011	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs10161184	0.95[CHB][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];0.85[EUR][1000 genomes]
rs10161488	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10744218	0.90[EUR][1000 genomes]
rs10744242	0.81[CHB][hapmap]
rs10773090	0.85[CHB][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10773108	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10773117	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10773162	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10773230	0.81[CHB][hapmap]
rs10846714	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10846852	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10846871	0.91[ASN][1000 genomes]
rs10846899	0.82[ASN][1000 genomes]
rs10846912	1.00[CHB][hapmap];0.81[JPT][hapmap];0.90[EUR][1000 genomes]
rs10846968	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs11057514	0.83[EUR][1000 genomes]
rs11057522	0.85[CHB][hapmap];0.91[JPT][hapmap];0.82[EUR][1000 genomes]
rs11057686	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11057813	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11057819	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11058272	0.87[EUR][1000 genomes]
rs11058562	1.00[YRI][hapmap]
rs1129167	0.91[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.85[EUR][1000 genomes]
rs11503023	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11610303	0.81[CHB][hapmap];1.00[YRI][hapmap]
rs11830957	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12314537	0.90[EUR][1000 genomes]
rs12812332	0.95[CHB][hapmap];0.86[JPT][hapmap];0.90[EUR][1000 genomes]
rs12817342	0.86[CHB][hapmap];1.00[YRI][hapmap]
rs12818177	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12828876	0.84[EUR][1000 genomes]
rs12829449	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1392142	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1532579	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1553178	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2341438	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4356269	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs4758657	0.86[CHB][hapmap]
rs4758658	0.86[CHB][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap]
rs4758660	0.81[CHB][hapmap]
rs4758664	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4758665	0.83[EUR][1000 genomes]
rs4758692	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs4758693	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4758695	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs61021925	0.88[EUR][1000 genomes]
rs6416295	0.81[CHB][hapmap]
rs6488947	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6489014	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs6489051	0.81[CHB][hapmap]
rs7134381	0.81[CHB][hapmap]
rs7296680	0.86[CHB][hapmap]
rs7298839	0.82[CHB][hapmap]
rs7305360	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7311573	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs7313121	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7313284	0.81[JPT][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7953204	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7955241	0.82[ASN][1000 genomes]
rs7955513	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs7959550	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7961258	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7964981	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7970007	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7972832	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7973480	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7974160	0.81[CHB][hapmap];0.82[JPT][hapmap];0.84[EUR][1000 genomes]
rs7975492	0.91[CHB][hapmap];0.91[JPT][hapmap];0.84[EUR][1000 genomes]
rs7978119	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7978636	0.83[EUR][1000 genomes]
rs868181	0.90[CHB][hapmap];0.86[JPT][hapmap];0.82[EUR][1000 genomes]
rs9788228	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529868	chr12:121956483-122944265	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	173 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:122856400-122884200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr12:122860600-122905000	Weak transcription	Brain Germinal Matrix	brain
3	chr12:122862800-122895600	Weak transcription	Small Intestine	intestine
4	chr12:122863400-122884200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
5	chr12:122863400-122884600	Weak transcription	Ovary	ovary
6	chr12:122863400-122897400	Weak transcription	Fetal Brain Female	brain
7	chr12:122863400-122897800	Weak transcription	Brain Substantia Nigra	brain
8	chr12:122863800-122905000	Weak transcription	Dnd41	blood
9	chr12:122865200-122885000	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr12:122866600-122888400	Weak transcription	Gastric	stomach
11	chr12:122867000-122885000	Weak transcription	Esophagus	oesophagus
12	chr12:122870000-122884200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr12:122871200-122884200	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr12:122874600-122884200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr12:122878800-122888400	Weak transcription	Primary T cells from cord blood	blood
16	chr12:122879400-122884200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr12:122880200-122884800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr12:122882000-122884400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr12:122882000-122885000	Weak transcription	Lung	lung
20	chr12:122882800-122884600	Active TSS	Psoas Muscle	Psoas
21	chr12:122883200-122884200	Active TSS	Skeletal Muscle Female	skeletal muscle
22	chr12:122883200-122884400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr12:122883600-122884200	Enhancers	iPS-20b Cell Line	embryonic stem cell
24	chr12:122883600-122884200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr12:122883600-122884200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr12:122883600-122884200	Enhancers	Pancreatic Islets	Pancreatic Islet
27	chr12:122883600-122884200	Enhancers	Stomach Mucosa	stomach
28	chr12:122883600-122884400	Genic enhancers	NHEK	skin
29	chr12:122883600-122884600	Active TSS	Right Ventricle	heart
30	chr12:122883600-122884800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr12:122883600-122884800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr12:122883600-122884800	Flanking Active TSS	Liver	Liver
33	chr12:122883600-122885000	Flanking Active TSS	A549	lung
34	chr12:122883600-122885200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr12:122883600-122885200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr12:122883600-122885200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
37	chr12:122883600-122885200	Flanking Active TSS	Hela-S3	cervix
38	chr12:122883600-122885200	Flanking Active TSS	K562	blood
39	chr12:122883600-122885400	Enhancers	Primary hematopoietic stem cells short term culture	blood
40	chr12:122883600-122885400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
41	chr12:122883600-122885400	Enhancers	Primary T helper cells fromperipheralblood	blood
42	chr12:122883600-122885400	Enhancers	Fetal Heart	heart
43	chr12:122883600-122885600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr12:122883800-122884200	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
45	chr12:122883800-122884200	Enhancers	H1 Cell Line	embryonic stem cell
46	chr12:122883800-122884200	Enhancers	HUES6 Cell Line	embryonic stem cell
47	chr12:122883800-122884200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
48	chr12:122883800-122884200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr12:122883800-122884200	Active TSS	Aorta	Aorta
50	chr12:122883800-122884200	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum

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