Variant report

Variant	rs11065212
Chromosome Location	chr12:121124307-121124308
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	SP1	chr12:121123961-121125120	GM12878	blood:	n/a	chr12:121124554-121124564 chr12:121124348-121124362 chr12:121124194-121124206 chr12:121124354-121124368 chr12:121124538-121124547 chr12:121124553-121124565 chr12:121124358-121124368 chr12:121124554-121124564 chr12:121124351-121124363 chr12:121124195-121124204 chr12:121124351-121124363 chr12:121124195-121124209 chr12:121124357-121124369 chr12:121124821-121124842 chr12:121124359-121124368 chr12:121124553-121124565 chr12:121124358-121124368 chr12:121124295-121124316 chr12:121124352-121124361 chr12:121124194-121124206 chr12:121124359-121124368 chr12:121124358-121124367 chr12:121124357-121124369 chr12:121124537-121124548 chr12:121124869-121124890
2	ELK1	chr12:121124178-121124878	K562	blood:	n/a	chr12:121124597-121124606 chr12:121124597-121124606
3	ELF1	chr12:121124005-121125139	SK-N-SH	brain:	n/a	chr12:121124211-121124223 chr12:121124158-121124167 chr12:121124593-121124606
4	NRF1	chr12:121124015-121124958	GM12878	blood:	n/a	chr12:121124749-121124760 chr12:121124778-121124789 chr12:121124776-121124790 chr12:121124747-121124761 chr12:121124358-121124367
5	POLR2A	chr12:121123935-121125383	GM12878	blood:	n/a	n/a
6	REST	chr12:121123942-121124512	SK-N-SH	brain:	n/a	n/a
7	IRF4	chr12:121124144-121124919	GM12878	blood:	n/a	n/a
8	NFYB	chr12:121124131-121125047	Hela-S3	cervix:	n/a	chr12:121124817-121124832 chr12:121124877-121124891 chr12:121124880-121124892 chr12:121124820-121124834 chr12:121124303-121124317 chr12:121124878-121124893 chr12:121124822-121124832 chr12:121124820-121124835 chr12:121124878-121124891 chr12:121124820-121124835 chr12:121124876-121124891 chr12:121124879-121124889 chr12:121124876-121124891
9	TCF3	chr12:121123937-121125123	GM12878	blood:	n/a	n/a
10	NFYA	chr12:121124077-121125090	Hela-S3	cervix:	n/a	chr12:121124820-121124838 chr12:121124877-121124891 chr12:121124880-121124892 chr12:121124820-121124834 chr12:121124303-121124317 chr12:121124872-121124890 chr12:121124822-121124832 chr12:121124820-121124835 chr12:121124878-121124891 chr12:121124820-121124835 chr12:121124876-121124891 chr12:121124879-121124889 chr12:121124876-121124891
11	TAF1	chr12:121123954-121124326	Hela-S3	cervix:	n/a	n/a
12	E2F6	chr12:121123874-121125271	A549	lung:	n/a	chr12:121124822-121124831 chr12:121124808-121124815 chr12:121124358-121124367 chr12:121124880-121124889 chr12:121125000-121125009 chr12:121124542-121124549 chr12:121124542-121124549 chr12:121124808-121124815 chr12:121125070-121125080 chr12:121124783-121124793 chr12:121124542-121124549 chr12:121124808-121124815 chr12:121124911-121124920 chr12:121124807-121124819 chr12:121124538-121124550
13	NFATC1	chr12:121123827-121124965	GM12878	blood:	n/a	n/a
14	TBL1XR1	chr12:121123996-121125246	GM12878	blood:	n/a	n/a
15	POLR2A	chr12:121123863-121125281	ECC-1	luminal epithelium:	n/a	n/a
16	EBF1	chr12:121124003-121124831	GM12878	blood:	n/a	chr12:121124388-121124399 chr12:121124389-121124398 chr12:121124372-121124385 chr12:121124372-121124383
17	CEBPB	chr12:121124083-121124851	Hela-S3	cervix:	n/a	chr12:121124823-121124831
18	RELA	chr12:121123976-121125154	GM19193	blood:	n/a	n/a
19	EP300	chr12:121124010-121125016	A549	lung:	n/a	chr12:121124598-121124605 chr12:121124737-121124750 chr12:121124158-121124167
20	CHD2	chr12:121123986-121125065	K562	blood:	n/a	n/a
21	EP300	chr12:121124266-121124484	GM12878	blood:	n/a	n/a
22	GABPA	chr12:121123991-121125529	K562	blood:	n/a	chr12:121124776-121124790 chr12:121124747-121124761 chr12:121124358-121124367
23	MAX	chr12:121124005-121125234	SK-N-SH	brain:	n/a	chr12:121124356-121124366 chr12:121124231-121124240 chr12:121124897-121124907 chr12:121124536-121124546 chr12:121124235-121124244
24	HA-E2F1	chr12:121123979-121125371	Hela-S3	cervix:	n/a	chr12:121124822-121124831 chr12:121124808-121124815 chr12:121124358-121124367 chr12:121124880-121124889 chr12:121125000-121125009 chr12:121124542-121124549 chr12:121124542-121124549 chr12:121124808-121124815 chr12:121125070-121125080 chr12:121124783-121124793 chr12:121124542-121124549 chr12:121124808-121124815 chr12:121124911-121124920 chr12:121124807-121124819 chr12:121124538-121124550
25	SP1	chr12:121123921-121125113	K562	blood:	n/a	chr12:121124554-121124564 chr12:121124348-121124362 chr12:121124194-121124206 chr12:121124354-121124368 chr12:121124538-121124547 chr12:121124553-121124565 chr12:121124358-121124368 chr12:121124554-121124564 chr12:121124351-121124363 chr12:121124195-121124204 chr12:121124351-121124363 chr12:121124195-121124209 chr12:121124357-121124369 chr12:121124821-121124842 chr12:121124359-121124368 chr12:121124553-121124565 chr12:121124358-121124368 chr12:121124295-121124316 chr12:121124352-121124361 chr12:121124194-121124206 chr12:121124359-121124368 chr12:121124358-121124367 chr12:121124357-121124369 chr12:121124537-121124548 chr12:121124869-121124890
26	ZNF143	chr12:121123891-121124864	K562	blood:	n/a	chr12:121124153-121124163
27	FOSL2	chr12:121124034-121125166	HepG2	liver:	n/a	chr12:121124824-121124833 chr12:121124878-121124887
28	POLR2A	chr12:121124056-121125155	HepG2	liver:	n/a	n/a
29	RCOR1	chr12:121123889-121124926	GM12878	blood:	n/a	n/a
30	POLR2A	chr12:121123847-121125154	GM12892	blood:	n/a	n/a
31	TAF1	chr12:121123849-121125328	A549	lung:	n/a	n/a
32	POLR2A	chr12:121123963-121125046	K562	blood:	n/a	n/a
33	SIN3AK20	chr12:121123902-121125465	H1-hESC	embryonic stem cell:	n/a	n/a
34	MAX	chr12:121123972-121125123	GM12878	blood:	n/a	chr12:121124356-121124366 chr12:121124231-121124240 chr12:121124897-121124907 chr12:121124536-121124546 chr12:121124235-121124244
35	POLR2A	chr12:121123940-121124488	A549	lung:	n/a	n/a
36	MEF2A	chr12:121124183-121124924	GM12878	blood:	n/a	n/a
37	POLR2A	chr12:121123914-121125249	GM12878	blood:	n/a	n/a
38	CEBPB	chr12:121124137-121124921	GM12878	blood:	n/a	chr12:121124880-121124888 chr12:121124823-121124831
39	YY1	chr12:121123954-121125409	K562	blood:	n/a	chr12:121124358-121124367 chr12:121125396-121125407 chr12:121124904-121124915 chr12:121124152-121124166 chr12:121124911-121124920 chr12:121124355-121124369
40	HEY1	chr12:121124271-121125122	HepG2	liver:	n/a	chr12:121124685-121124700 chr12:121124901-121124916
41	HEY1	chr12:121123924-121125241	K562	blood:	n/a	chr12:121124685-121124700 chr12:121124901-121124916
42	EGR1	chr12:121124134-121124805	H1-hESC	embryonic stem cell:	n/a	chr12:121124532-121124547 chr12:121124597-121124606 chr12:121124358-121124368 chr12:121124352-121124367 chr12:121124355-121124365 chr12:121124707-121124716 chr12:121124533-121124546 chr12:121124353-121124366 chr12:121124429-121124443 chr12:121124555-121124570 chr12:121124533-121124546 chr12:121124353-121124366
43	SIN3A	chr12:121124072-121125381	GM12878	blood:	n/a	chr12:121125003-121125016 chr12:121124872-121124881 chr12:121124904-121124915
44	MXI1	chr12:121123504-121126465	IMR90	lung:	n/a	chr12:121124229-121124244 chr12:121124231-121124246
45	BRCA1	chr12:121123883-121124977	Hela-S3	cervix:	n/a	n/a
46	POLR2A	chr12:121123884-121125445	H1-neurons	neurons:	n/a	n/a
47	POLR2A	chr12:121123877-121125410	MCF-7	breast:	n/a	n/a
48	SRF	chr12:121123826-121125198	MCF-7	breast:	n/a	chr12:121124867-121124877 chr12:121124356-121124366 chr12:121124536-121124546
49	POLR2A	chr12:121123809-121125369	U87	brain:	n/a	n/a
50	POLR2A	chr12:121123978-121124329	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:121122795..121124642-chr12:121341145..121343288,2	MCF-7	breast:
2	chr12:121095512..121100910-chr12:121122531..121126551,5	MCF-7	breast:
3	chr12:121123033..121125000-chr12:121205934..121208435,2	K562	blood:
4	chr12:121085946..121088715-chr12:121122622..121126229,3	K562	blood:
5	chr12:121122674..121127779-chr12:121131254..121137297,11	MCF-7	breast:
6	chr12:121018631..121021385-chr12:121124185..121125689,2	MCF-7	breast:
7	chr12:120875946..120878903-chr12:121123173..121125911,2	K562	blood:
8	chr12:120728399..120731246-chr12:121124112..121127371,3	MCF-7	breast:
9	chr12:121122826..121126231-chr12:121135368..121138328,4	MCF-7	breast:
10	chr12:121122617..121126013-chr12:121146742..121149972,4	MCF-7	breast:
11	chr12:121123292..121126341-chr12:121146632..121149740,5	MCF-7	breast:
12	chr12:121017632..121023235-chr12:121123750..121127979,5	K562	blood:
13	chr12:121122969..121126872-chr12:121145365..121151601,10	K562	blood:
14	chr12:120630041..120632673-chr12:121124063..121125965,2	MCF-7	breast:
15	chr12:121085923..121088804-chr12:121121977..121126483,5	MCF-7	breast:

Variant related genes	Relation type
MLEC	TF binding region
ENSG00000111780	Chromatin interaction
ENSG00000089154	Chromatin interaction
ENSG00000110917	Chromatin interaction
ENSG00000202538	Chromatin interaction
ENSG00000200795	Chromatin interaction
ENSG00000157837	Chromatin interaction
ENSG00000175970	Chromatin interaction
ENSG00000167272	Chromatin interaction
ENSG00000111775	Chromatin interaction
ENSG00000157782	Chromatin interaction
ENSG00000256364	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10849779	0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs11065208	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs11065211	1.00[ASW][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11065230	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11065270	0.85[JPT][hapmap]
rs11829037	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11833718	0.85[JPT][hapmap]
rs12296423	0.87[ASW][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.88[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12306138	0.85[JPT][hapmap]
rs1803508	0.97[ASN][1000 genomes]
rs3830155	0.94[AFR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4559761	0.93[ASW][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55644516	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs59358833	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59904018	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61229807	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6489783	0.85[JPT][hapmap]
rs6490302	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs695950	0.90[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs7133413	0.85[JPT][hapmap]
rs7135915	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7303170	0.80[ASW][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7307973	0.85[JPT][hapmap]
rs7309538	0.84[JPT][hapmap]
rs73409923	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7956685	0.89[EUR][1000 genomes]
rs7958698	1.00[ASW][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7960336	0.85[JPT][hapmap]
rs7964228	0.85[ASN][1000 genomes]
rs7972583	0.90[ASN][1000 genomes]
rs7972912	0.85[JPT][hapmap]
rs7973907	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs949443	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv521928	chr12:121041728-121761800	Genic enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
2	nsv899557	chr12:121069201-121189116	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh 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 miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv1037070	chr12:121069938-121459047	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
4	nsv1045923	chr12:121082203-121146219	Strong transcription Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 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	chr12:121123600-121125600	Active TSS	Fetal Brain Female	brain
2	chr12:121123600-121125800	Active TSS	K562	blood
3	chr12:121123600-121126000	Active TSS	HUES48 Cell Line	embryonic stem cell
4	chr12:121123600-121126400	Active TSS	HUES64 Cell Line	embryonic stem cell
5	chr12:121123600-121126600	Active TSS	HUES6 Cell Line	embryonic stem cell
6	chr12:121123600-121126600	Active TSS	iPS-20b Cell Line	embryonic stem cell
7	chr12:121123600-121126600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr12:121123600-121127000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr12:121123600-121127000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr12:121123800-121124600	Flanking Active TSS	Primary B cells from cord blood	blood
11	chr12:121123800-121124600	Flanking Active TSS	Adipose Nuclei	Adipose
12	chr12:121123800-121124600	Active TSS	Fetal Brain Male	brain
13	chr12:121123800-121124600	Active TSS	Right Atrium	heart
14	chr12:121123800-121125000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr12:121123800-121125000	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
16	chr12:121123800-121125400	Active TSS	Brain Cingulate Gyrus	brain
17	chr12:121123800-121125600	Active TSS	Brain Angular Gyrus	brain
18	chr12:121123800-121125600	Active TSS	Brain Germinal Matrix	brain
19	chr12:121123800-121125600	Active TSS	Brain Substantia Nigra	brain
20	chr12:121123800-121125600	Active TSS	Placenta	Placenta
21	chr12:121123800-121125800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr12:121123800-121125800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
23	chr12:121123800-121125800	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr12:121123800-121125800	Active TSS	Brain Hippocampus Middle	brain
25	chr12:121123800-121125800	Active TSS	Brain Inferior Temporal Lobe	brain
26	chr12:121123800-121125800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
27	chr12:121123800-121125800	Active TSS	Rectal Smooth Muscle	rectum
28	chr12:121123800-121125800	Active TSS	HSMMtube	muscle
29	chr12:121123800-121126000	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr12:121123800-121126000	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr12:121123800-121126000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr12:121123800-121126000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr12:121123800-121126000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr12:121123800-121126000	Active TSS	Colon Smooth Muscle	Colon
35	chr12:121123800-121126000	Active TSS	Fetal Kidney	kidney
36	chr12:121123800-121126000	Active TSS	Right Ventricle	heart
37	chr12:121123800-121126000	Active TSS	Thymus	Thymus
38	chr12:121123800-121126200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr12:121123800-121126200	Active TSS	Breast Myoepithelial Primary Cells	Breast
40	chr12:121123800-121126200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr12:121123800-121126200	Active TSS	NHEK	skin
42	chr12:121123800-121126400	Active TSS	NHLF	lung
43	chr12:121123800-121126600	Active TSS	Aorta	Aorta
44	chr12:121123800-121126600	Active TSS	Left Ventricle	heart
45	chr12:121123800-121126600	Active TSS	Ovary	ovary
46	chr12:121123800-121126600	Active TSS	Psoas Muscle	Psoas
47	chr12:121123800-121126600	Active TSS	Sigmoid Colon	Sigmoid Colon
48	chr12:121123800-121126600	Active TSS	Small Intestine	intestine
49	chr12:121123800-121126800	Active TSS	ES-I3 Cell Line	embryonic stem cell
50	chr12:121123800-121126800	Active TSS	H1 Cell Line	embryonic stem cell

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