Variant report

Variant	rs12205957
Chromosome Location	chr6:74233621-74233622
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:395)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:395 , 50 per page) page: 1 2 3 4 5 6 7 8

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOXM1	chr6:74233046-74233817	GM12878	blood:	n/a	n/a
2	HDAC2	chr6:74233279-74233644	K562	blood:	n/a	n/a
3	CEBPD	chr6:74233156-74233686	HepG2	liver:	n/a	n/a
4	USF1	chr6:74233390-74233716	A549	lung:	n/a	n/a
5	EP300	chr6:74233422-74233986	GM12878	blood:	n/a	chr6:74233695-74233709
6	POLR2A	chr6:74233228-74233725	A549	lung:	n/a	n/a
7	TBL1XR1	chr6:74233302-74233868	K562	blood:	n/a	n/a
8	HEY1	chr6:74233040-74233802	HepG2	liver:	n/a	n/a
9	RFX5	chr6:74233337-74233682	GM12878	blood:	n/a	n/a
10	POLR2A	chr6:74233007-74233878	Hela-S3	cervix:	n/a	n/a
11	MYC	chr6:74233073-74233881	K562	blood:	n/a	n/a
12	GABPA	chr6:74233049-74233899	A549	lung:	n/a	chr6:74233318-74233327
13	MYC	chr6:74232687-74234001	K562	blood:	n/a	n/a
14	TAF1	chr6:74233080-74233806	GM12878	blood:	n/a	n/a
15	NFIC	chr6:74232897-74233996	GM12878	blood:	n/a	n/a
16	RUNX3	chr6:74233070-74233922	GM12878	blood:	n/a	n/a
17	MAZ	chr6:74233046-74233993	GM12878	blood:	n/a	n/a
18	NFIC	chr6:74233313-74233691	HepG2	liver:	n/a	n/a
19	POLR2A	chr6:74233047-74233791	H1-hESC	embryonic stem cell:	n/a	n/a
20	RELA	chr6:74233068-74233776	GM18951	blood:	n/a	n/a
21	CBX3	chr6:74232672-74233781	K562	blood:	n/a	n/a
22	IRF1	chr6:74232662-74234107	K562	blood:	n/a	n/a
23	MAZ	chr6:74233090-74233697	HepG2	liver:	n/a	n/a
24	REST	chr6:74233163-74233855	HL-60	blood:	n/a	n/a
25	POLR2A	chr6:74232667-74234114	K562	blood:	n/a	n/a
26	TAF1	chr6:74233374-74233737	GM12878	blood:	n/a	n/a
27	POLR2A	chr6:74233008-74233727	GM12878	blood:	n/a	n/a
28	USF2	chr6:74233422-74234002	Hela-S3	cervix:	n/a	chr6:74233616-74233627
29	ELF1	chr6:74232977-74233717	GM12878	blood:	n/a	n/a
30	TAF1	chr6:74233224-74233703	GM12891	blood:	n/a	n/a
31	CCNT2	chr6:74233191-74233633	K562	blood:	n/a	chr6:74233264-74233273
32	RAD21	chr6:74233365-74233704	H1-hESC	embryonic stem cell:	n/a	n/a
33	YY1	chr6:74233058-74233688	K562	blood:	n/a	chr6:74233264-74233275
34	STAT3	chr6:74233473-74233637	MCF10A-Er-Src	breast:	n/a	n/a
35	POLR2A	chr6:74233341-74233715	H1-hESC	embryonic stem cell:	n/a	n/a
36	TCF3	chr6:74233167-74233653	GM12878	blood:	n/a	n/a
37	KAP1	chr6:74232741-74234215	HEK293	kidney:	n/a	n/a
38	POLR2A	chr6:74232596-74233967	K562	blood:	n/a	n/a
39	YY1	chr6:74233051-74233644	HepG2	liver:	n/a	chr6:74233264-74233275
40	POLR2A	chr6:74233109-74233978	HUVEC	blood vessel:	n/a	n/a
41	RCOR1	chr6:74233171-74233862	GM12878	blood:	n/a	n/a
42	MBD4	chr6:74233276-74233850	HepG2	liver:	n/a	n/a
43	JUND	chr6:74233453-74233653	H1-hESC	embryonic stem cell:	n/a	n/a
44	POLR2A	chr6:74233033-74233758	HepG2	liver:	n/a	n/a
45	MAFF	chr6:74233556-74233998	K562	blood:	n/a	n/a
46	REST	chr6:74233013-74233749	K562	blood:	n/a	n/a
47	CTCF	chr6:74233480-74233630	HRE	kidney:	n/a	n/a
48	SIN3AK20	chr6:74233083-74233902	MCF-7	breast:	n/a	n/a
49	EGR1	chr6:74233207-74233662	GM12878	blood:	n/a	n/a
50	POLR2A	chr6:74233189-74233819	HUVEC	blood vessel:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:74221323..74236726-chr6:74306065..74338770,101	K562	blood:
2	chr6:74228067..74234767-chr6:74357105..74365312,16	MCF-7	breast:
3	chr6:74231501..74234013-chr6:75953624..75956455,2	MCF-7	breast:
4	chr6:74219718..74234750-chr6:74354945..74369231,56	K562	blood:
5	chr6:74220976..74234980-chr6:74352572..74366941,62	K562	blood:
6	chr6:74233083..74233652-chr7:5820678..5821633,2	Hela-S3	cervix:
7	chr19:1026112..1026717-chr6:74233509..74234038,2	HCT-116	colon:
8	chr6:74232912..74233717-chr7:154794709..154795565,2	NB4	blood:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MTO1-1	chr6:74233564-74233631	ENSG00000229862.1

No data

Variant related genes	Relation type
EEF1A1	TF binding region
ENSG00000157212	Chromatin interaction
ENSG00000218459	Chromatin interaction
ENSG00000273344	Chromatin interaction
ENSG00000064666	Chromatin interaction
ENSG00000011275	Chromatin interaction
ENSG00000112695	Chromatin interaction
ENSG00000119899	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10943103	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11963033	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11965436	0.81[AMR][1000 genomes]
rs12190444	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12191112	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12193628	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12197170	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12198839	0.91[EUR][1000 genomes]
rs12199142	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12199577	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12205991	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12212315	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs28365878	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3857464	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3857465	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4302642	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56104432	0.96[EUR][1000 genomes]
rs56375536	1.00[EUR][1000 genomes]
rs72947408	1.00[EUR][1000 genomes]
rs72947410	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72960049	0.81[AMR][1000 genomes]
rs72961942	0.81[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3410973	chr6:73716033-74419545	Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	191 gene(s)	inside rSNPs	diseases
2	nsv886158	chr6:74126084-74436825	Weak transcription Active TSS Strong transcription Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	179 gene(s)	inside rSNPs	diseases
3	nsv1027968	chr6:74155378-74521923	Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	178 gene(s)	inside rSNPs	diseases
4	nsv538305	chr6:74155378-74521923	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	178 gene(s)	inside rSNPs	diseases
5	nsv1017716	chr6:74173173-74401162	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases
6	nsv1023250	chr6:74189642-74605976	Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	172 gene(s)	inside rSNPs	diseases
7	nsv538306	chr6:74189642-74605976	Strong transcription Enhancers Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	172 gene(s)	inside rSNPs	diseases
8	esv2763576	chr6:74197638-74277249	Strong transcription Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	160 gene(s)	inside rSNPs	diseases
9	nsv5350	chr6:74221995-74267088	Active TSS Flanking Active TSS Genic enhancers Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	159 gene(s)	inside rSNPs	diseases
10	nsv886159	chr6:74223153-74275405	Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	159 gene(s)	inside rSNPs	diseases
11	nsv463153	chr6:74229258-74290291	Weak transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	141 gene(s)	inside rSNPs	diseases
12	nsv603693	chr6:74229258-74290291	Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	141 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:74227800-74233800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr6:74230000-74233800	Active TSS	HSMM	muscle
3	chr6:74230000-74233800	Active TSS	K562	blood
4	chr6:74230800-74234200	Active TSS	ES-I3 Cell Line	embryonic stem cell
5	chr6:74231400-74234200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
6	chr6:74231600-74234400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr6:74232200-74233800	Active TSS	HUES6 Cell Line	embryonic stem cell
8	chr6:74232200-74233800	Active TSS	HSMMtube	muscle
9	chr6:74232200-74234000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr6:74232200-74234000	Active TSS	Duodenum Smooth Muscle	Duodenum
11	chr6:74232400-74233800	Active TSS	iPS-15b Cell Line	embryonic stem cell
12	chr6:74232400-74233800	Active TSS	Stomach Mucosa	stomach
13	chr6:74232600-74233800	Flanking Active TSS	Fetal Muscle Leg	muscle
14	chr6:74232600-74234000	Flanking Active TSS	HUVEC	blood vessel
15	chr6:74232600-74234200	Flanking Active TSS	Primary hematopoietic stem cells	blood
16	chr6:74232600-74234400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr6:74232800-74233800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
18	chr6:74232800-74233800	Active TSS	Primary T helper naive cells from peripheral blood	blood
19	chr6:74232800-74233800	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
20	chr6:74232800-74233800	Active TSS	Primary T killer memory cells from peripheral blood	blood
21	chr6:74232800-74233800	Active TSS	Esophagus	oesophagus
22	chr6:74232800-74233800	Active TSS	Rectal Mucosa Donor 29	rectum
23	chr6:74232800-74233800	Active TSS	Right Atrium	heart
24	chr6:74232800-74233800	Active TSS	Small Intestine	intestine
25	chr6:74232800-74234000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr6:74232800-74234000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
27	chr6:74232800-74234000	Active TSS	Brain Anterior Caudate	brain
28	chr6:74232800-74234000	Active TSS	Colonic Mucosa	Colon
29	chr6:74232800-74234000	Active TSS	Colon Smooth Muscle	Colon
30	chr6:74232800-74234000	Active TSS	Fetal Adrenal Gland	Adrenal Gland
31	chr6:74232800-74234000	Active TSS	Fetal Stomach	stomach
32	chr6:74233000-74233800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr6:74233000-74233800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr6:74233000-74233800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr6:74233000-74233800	Active TSS	Primary T cells from cord blood	blood
36	chr6:74233000-74233800	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
37	chr6:74233000-74233800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr6:74233000-74233800	Enhancers	Cortex derived primary cultured neurospheres	brain
39	chr6:74233000-74233800	Active TSS	Aorta	Aorta
40	chr6:74233000-74233800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
41	chr6:74233000-74233800	Active TSS	Fetal Kidney	kidney
42	chr6:74233000-74233800	Active TSS	Lung	lung
43	chr6:74233000-74233800	Active TSS	Ovary	ovary
44	chr6:74233000-74233800	Active TSS	Pancreas	Pancrea
45	chr6:74233000-74233800	Active TSS	Placenta Amnion	Placenta Amnion
46	chr6:74233000-74233800	Bivalent/Poised TSS	Psoas Muscle	Psoas
47	chr6:74233000-74233800	Active TSS	Sigmoid Colon	Sigmoid Colon
48	chr6:74233000-74233800	Active TSS	Hela-S3	cervix
49	chr6:74233000-74233800	Active TSS	Osteobl	bone
50	chr6:74233000-74234000	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung

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