Variant report

Variant	rs12190970
Chromosome Location	chr6:11093444-11093445
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	ZNF143	chr6:11093376-11094505	K562	blood:	n/a	chr6:11093935-11093944 chr6:11093924-11093939 chr6:11093987-11094005 chr6:11093923-11093942 chr6:11093937-11093946 chr6:11093928-11093946
2	CEBPB	chr6:11093251-11095508	Hela-S3	cervix:	n/a	n/a
3	CTCF	chr6:11093400-11093550	AG04449	skin:	n/a	n/a
4	CREB1	chr6:11093322-11095204	HepG2	liver:	n/a	n/a
5	IRF1	chr6:11093371-11094378	K562	blood:	n/a	n/a
6	POLR2A	chr6:11093225-11095032	Hela-S3	cervix:	n/a	n/a
7	SRF	chr6:11093317-11094341	MCF-7	breast:	n/a	n/a
8	MYC	chr6:11093379-11095544	K562	blood:	n/a	chr6:11095020-11095029 chr6:11095376-11095387 chr6:11095377-11095384
9	POLR2A	chr6:11093251-11094327	GM12878	blood:	n/a	n/a
10	TEAD4	chr6:11093234-11095560	K562	blood:	n/a	n/a
11	JUND	chr6:11093331-11095200	K562	blood:	n/a	n/a
12	SPI1	chr6:11093187-11093509	GM12891	blood:	n/a	n/a
13	MAX	chr6:11093292-11095012	MCF-7	breast:	n/a	n/a
14	TFAP2A	chr6:11093318-11095008	Hela-S3	cervix:	n/a	chr6:11094807-11094815 chr6:11094290-11094305 chr6:11093509-11093520 chr6:11093652-11093666
15	SMC3	chr6:11093274-11095060	Hela-S3	cervix:	n/a	n/a
16	TCF7L2	chr6:11093330-11094596	PANC-1	pancreas:	n/a	n/a
17	HEY1	chr6:11093410-11094935	HepG2	liver:	n/a	n/a
18	CTCF	chr6:11093360-11093510	SK-N-SH_RA	brain:	n/a	n/a
19	POLR2A	chr6:11093238-11095117	GM12878	blood:	n/a	n/a
20	POLR2A	chr6:11093323-11094630	PFSK-1	brain:	n/a	n/a
21	POLR2A	chr6:11093235-11095157	Hela-S3	cervix:	n/a	n/a
22	HEY1	chr6:11093353-11094684	HepG2	liver:	n/a	n/a
23	MAX	chr6:11093430-11095444	A549	lung:	n/a	chr6:11095020-11095029 chr6:11095376-11095387 chr6:11095377-11095384
24	ZMIZ1	chr6:11093420-11094648	K562	blood:	n/a	n/a
25	POLR2A	chr6:11093232-11095122	GM12892	blood:	n/a	n/a
26	MAX	chr6:11093258-11095135	K562	blood:	n/a	chr6:11095020-11095029
27	POLR2A	chr6:11093070-11095095	GM19099	blood:	n/a	n/a
28	HCFC1	chr6:11093050-11095342	K562	blood:	n/a	n/a
29	POLR2A	chr6:11093400-11094830	GM12878	blood:	n/a	n/a
30	CTCF	chr6:11093440-11093590	Hela-S3	cervix:	n/a	n/a
31	ELK1	chr6:11093370-11094139	GM12878	blood:	n/a	n/a
32	RAD21	chr6:11093328-11095178	IMR90	lung:	n/a	n/a
33	MAFK	chr6:11093392-11094353	Hela-S3	cervix:	n/a	n/a
34	RELA	chr6:11093277-11095093	GM15510	blood:	n/a	n/a
35	POLR2A	chr6:11093340-11093534	GM12878	blood:	n/a	n/a
36	POLR2A	chr6:11093263-11095075	GM12891	blood:	n/a	n/a
37	MAFK	chr6:11093408-11094105	K562	blood:	n/a	n/a
38	RCOR1	chr6:11093199-11094300	K562	blood:	n/a	n/a
39	CTCF	chr6:11093240-11093510	Caco-2	colon:	n/a	n/a
40	MAX	chr6:11093386-11095509	NB4	blood:	n/a	chr6:11095020-11095029 chr6:11095376-11095387 chr6:11095377-11095384
41	ATF2	chr6:11093222-11094151	GM12878	blood:	n/a	n/a
42	USF2	chr6:11093443-11093599	HepG2	liver:	n/a	n/a
43	E2F6	chr6:11093402-11095019	K562	blood:	n/a	chr6:11094329-11094340
44	MBD4	chr6:11093313-11094082	HepG2	liver:	n/a	n/a
45	MAX	chr6:11093404-11094985	GM12878	blood:	n/a	n/a
46	POLR2A	chr6:11093372-11095068	H1-neurons	neurons:	n/a	n/a
47	HCFC1	chr6:11092962-11095589	Hela-S3	cervix:	n/a	n/a
48	POLR2A	chr6:11093260-11094219	GM12891	blood:	n/a	n/a
49	MAX	chr6:11093104-11095896	Hela-S3	cervix:	n/a	chr6:11095020-11095029 chr6:11095376-11095387 chr6:11095377-11095384
50	POLR2A	chr6:11093234-11095441	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:11076830..11080568-chr6:11090917..11093944,4	K562	blood:
2	chr6:11093400..11095150-chr6:11232098..11234841,2	MCF-7	breast:
3	chr1:109234578..109235412-chr6:11093147..11094128,2	Hela-S3	cervix:
4	chr6:10874568..10876726-chr6:11092303..11094162,2	MCF-7	breast:
5	chr15:71406155..71408643-chr6:11092214..11094217,2	MCF-7	breast:
6	chr6:11093374..11093896-chr9:133454393..133454965,2	NB4	blood:
7	chr6:11092829..11095210-chr6:11111953..11113686,2	K562	blood:

Variant related genes	Relation type
SMIM13	TF binding region
ENSG00000244476	Chromatin interaction
ENSG00000134186	Chromatin interaction
ENSG00000238896	Chromatin interaction
ENSG00000225362	Chromatin interaction
ENSG00000111859	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10484446	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10484448	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10946967	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10946968	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10947002	0.81[ASN][1000 genomes]
rs11751998	0.81[ASN][1000 genomes]
rs11759939	0.90[ASN][1000 genomes]
rs12193702	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12194681	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12199551	0.81[ASN][1000 genomes]
rs12200717	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12200932	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12205389	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12211539	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12212683	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12213689	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12215910	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4711180	0.82[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs6456846	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1021078	chr6:10819083-11558560	Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv538135	chr6:10819083-11558560	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 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	chr6:11092800-11096000	Active TSS	iPS-20b Cell Line	embryonic stem cell
2	chr6:11093000-11093600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr6:11093000-11093600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr6:11093000-11093600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr6:11093000-11093600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr6:11093000-11093600	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
7	chr6:11093000-11093600	Flanking Active TSS	Dnd41	blood
8	chr6:11093000-11093800	Flanking Active TSS	Primary hematopoietic stem cells	blood
9	chr6:11093000-11094800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr6:11093000-11094800	Active TSS	Fetal Lung	lung
11	chr6:11093000-11095000	Active TSS	Rectal Mucosa Donor 29	rectum
12	chr6:11093000-11095400	Active TSS	Pancreatic Islets	Pancreatic Islet
13	chr6:11093000-11095600	Active TSS	Breast Myoepithelial Primary Cells	Breast
14	chr6:11093000-11095800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr6:11093000-11095800	Active TSS	HMEC	breast
16	chr6:11093000-11096000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr6:11093000-11096000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr6:11093000-11096000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr6:11093000-11096000	Active TSS	A549	lung
20	chr6:11093000-11096400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr6:11093000-11096400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
22	chr6:11093000-11096400	Active TSS	GM12878-XiMat	blood
23	chr6:11093000-11096600	Active TSS	HUES6 Cell Line	embryonic stem cell
24	chr6:11093200-11093600	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
25	chr6:11093200-11093600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr6:11093200-11093600	Flanking Active TSS	Primary B cells from cord blood	blood
27	chr6:11093200-11093600	Flanking Active TSS	Primary B cells from peripheral blood	blood
28	chr6:11093200-11093600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
29	chr6:11093200-11093600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
30	chr6:11093200-11093600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
31	chr6:11093200-11093600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
32	chr6:11093200-11093600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
33	chr6:11093200-11093600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
34	chr6:11093200-11093600	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr6:11093200-11093600	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
36	chr6:11093200-11093600	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
37	chr6:11093200-11093600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
38	chr6:11093200-11093600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr6:11093200-11093600	Flanking Active TSS	Liver	Liver
40	chr6:11093200-11093600	Flanking Active TSS	Colon Smooth Muscle	Colon
41	chr6:11093200-11093600	Flanking Active TSS	Duodenum Mucosa	Duodenum
42	chr6:11093200-11093600	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
43	chr6:11093200-11093600	Flanking Active TSS	Fetal Brain Female	brain
44	chr6:11093200-11093600	Flanking Active TSS	Fetal Muscle Leg	muscle
45	chr6:11093200-11093600	Flanking Active TSS	Fetal Thymus	thymus
46	chr6:11093200-11093600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
47	chr6:11093200-11093600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
48	chr6:11093200-11093600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
49	chr6:11093200-11093600	Flanking Active TSS	HSMMtube	muscle
50	chr6:11093200-11093600	Flanking Active TSS	NHDF-Ad	bronchial

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