Variant report

Variant	rs1061397
Chromosome Location	chr6:30692539-30692540
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:99)
CpG islands
(count:0)
Chromatin interactive
region (count:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:99 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:30692296-30694437	K562	blood:	n/a	n/a
2	PML	chr6:30692201-30694187	K562	blood:	n/a	n/a
3	POLR2A	chr6:30687742-30694690	GM12878	blood:	n/a	n/a
4	POLR2A	chr6:30692324-30694192	HCT-116	colon:	n/a	n/a
5	POLR2A	chr6:30690060-30695157	GM12892	blood:	n/a	n/a
6	SIN3AK20	chr6:30692384-30693148	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr6:30687036-30695449	HUVEC	blood vessel:	n/a	n/a
8	POLR2A	chr6:30690176-30694491	HepG2	liver:	n/a	n/a
9	POLR2A	chr6:30687122-30694167	H1-hESC	embryonic stem cell:	n/a	n/a
10	POLR2A	chr6:30692316-30694157	K562	blood:	n/a	n/a
11	POLR2A	chr6:30683610-30695318	SK-N-MC	brain:	n/a	n/a
12	POLR2A	chr6:30691230-30694189	K562	blood:	n/a	n/a
13	TEAD4	chr6:30692284-30694091	K562	blood:	n/a	n/a
14	MBD4	chr6:30692362-30694218	HepG2	liver:	n/a	n/a
15	POLR2A	chr6:30692454-30693107	H1-hESC	embryonic stem cell:	n/a	n/a
16	POLR2A	chr6:30692324-30694533	HCT-116	colon:	n/a	n/a
17	POLR2A	chr6:30690156-30694752	Hela-S3	cervix:	n/a	n/a
18	POLR2A	chr6:30690112-30695297	Hela-S3	cervix:	n/a	n/a
19	POLR2A	chr6:30686736-30693839	K562	blood:	n/a	n/a
20	POLR2A	chr6:30687488-30695337	Hela-S3	cervix:	n/a	n/a
21	SP1	chr6:30691119-30693317	H1-hESC	embryonic stem cell:	n/a	n/a
22	POLR2A	chr6:30692338-30695323	HUVEC	blood vessel:	n/a	n/a
23	POLR2A	chr6:30692209-30696227	U87	brain:	n/a	n/a
24	SIN3AK20	chr6:30692377-30693953	K562	blood:	n/a	n/a
25	POLR2A	chr6:30687419-30696083	PFSK-1	brain:	n/a	n/a
26	POLR2A	chr6:30692532-30694464	HL-60	blood:	n/a	n/a
27	POLR2A	chr6:30692488-30694436	U87	brain:	n/a	n/a
28	POLR2A	chr6:30687384-30694779	K562	blood:	n/a	n/a
29	POLR2A	chr6:30687265-30694784	K562	blood:	n/a	n/a
30	PML	chr6:30692136-30695252	GM12878	blood:	n/a	n/a
31	POLR2A	chr6:30690124-30695305	SK-N-MC	brain:	n/a	n/a
32	BCL3	chr6:30692369-30694191	A549	lung:	n/a	n/a
33	CEBPD	chr6:30692436-30694223	K562	blood:	n/a	n/a
34	CEBPB	chr6:30692536-30693825	K562	blood:	n/a	n/a
35	POLR2A	chr6:30692078-30695225	SK-N-SH	brain:	n/a	n/a
36	POLR2A	chr6:30692358-30694454	H1-neurons	neurons:	n/a	n/a
37	POLR2A	chr6:30690069-30695502	MCF-7	breast:	n/a	n/a
38	POLR2A	chr6:30690223-30696218	A549	lung:	n/a	n/a
39	MTA3	chr6:30692389-30695265	GM12878	blood:	n/a	n/a
40	POLR2A	chr6:30687113-30694561	H1-hESC	embryonic stem cell:	n/a	n/a
41	POLR2A	chr6:30687285-30695231	K562	blood:	n/a	n/a
42	POLR2A	chr6:30692414-30696242	ECC-1	luminal epithelium:	n/a	n/a
43	HEY1	chr6:30686545-30693356	K562	blood:	n/a	chr6:30689309-30689324 chr6:30689249-30689264 chr6:30689435-30689450 chr6:30689347-30689362
44	POLR2A	chr6:30686133-30696545	PANC-1	pancreas:	n/a	n/a
45	POLR2A	chr6:30692359-30694362	H1-neurons	neurons:	n/a	n/a
46	POLR2A	chr6:30690110-30694856	GM12891	blood:	n/a	n/a
47	POLR2A	chr6:30692409-30694167	HepG2	liver:	n/a	n/a
48	NFIC	chr6:30692286-30692936	HepG2	liver:	n/a	n/a
49	POLR2A	chr6:30692378-30695189	Hela-S3	cervix:	n/a	n/a
50	POLR2A	chr6:30692297-30695185	GM12878	blood:	n/a	n/a

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:30451219..30453103-chr6:30692483..30694829,2	K562	blood:
2	chr6:30691897..30694851-chr6:30760025..30762962,2	K562	blood:
3	chr6:30576582..30588788-chr6:30682721..30700088,114	K562	blood:
4	chr6:30634661..30668428-chr6:30680318..30698953,145	MCF-7	breast:
5	chr6:30608315..30616989-chr6:30683761..30694958,31	K562	blood:
6	chr6:30692214..30695086-chr6:30900554..30903279,2	K562	blood:
7	chr6:30692018..30694762-chr6:30878588..30881246,2	K562	blood:
8	chr6:30577862..30587208-chr6:30682997..30696247,43	MCF-7	breast:
9	chr6:30510952..30513795-chr6:30691840..30693915,2	K562	blood:
10	chr13:41956378..41959414-chr6:30690779..30694701,5	K562	blood:
11	chr6:30643326..30660432-chr6:30681522..30696111,127	MCF-7	breast:
12	chr6:30447631..30450065-chr6:30691817..30695001,3	K562	blood:
13	chr6:30577773..30589670-chr6:30680333..30700280,58	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000272540	TF binding region
ENSG00000146112	Chromatin interaction
ENSG00000204560	Chromatin interaction
ENSG00000266183	Chromatin interaction
ENSG00000204564	Chromatin interaction
ENSG00000204568	Chromatin interaction
ENSG00000222894	Chromatin interaction
ENSG00000137404	Chromatin interaction
ENSG00000214222	Chromatin interaction
ENSG00000204569	Chromatin interaction
ENSG00000137343	Chromatin interaction
ENSG00000230449	Chromatin interaction
ENSG00000213780	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1049943	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1061424	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10947088	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10947089	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1136719	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12111310	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1264352	0.83[ASN][1000 genomes]
rs15297	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17189329	0.85[ASN][1000 genomes]
rs17195712	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17719	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28600807	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3094128	0.97[ASN][1000 genomes]
rs3130662	1.00[ASN][1000 genomes]
rs3909184	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41270529	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58638768	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9968884	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9968888	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9968913	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9968960	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9969042	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3519970	chr6:30382942-31378788	Genic enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1030 gene(s)	inside rSNPs	diseases
2	esv3519971	chr6:30382942-31378788	Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1030 gene(s)	inside rSNPs	diseases
3	nsv601481	chr6:30422632-31284253	Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1012 gene(s)	inside rSNPs	diseases
4	esv3430377	chr6:30443802-30814426	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	967 gene(s)	inside rSNPs	diseases
5	nsv830626	chr6:30558064-30732905	Weak transcription Enhancers Active TSS Genic enhancers Strong transcription 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	406 gene(s)	inside rSNPs	diseases
6	esv2758041	chr6:30644693-30816319	Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	223 gene(s)	inside rSNPs	diseases
7	esv2759413	chr6:30644693-30816319	Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	223 gene(s)	inside rSNPs	diseases
8	nsv970104	chr6:30690935-30693035	Strong transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers Weak transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	19 gene(s)	inside rSNPs	diseases
9	nsv970736	chr6:30692055-30710740	Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	112 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1061397	LOC647000	trans	multi-tissue	Pritchard

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30688800-30693200	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr6:30689400-30693000	Transcr. at gene 5' and 3'	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr6:30689400-30693000	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr6:30689400-30694000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr6:30689400-30694000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr6:30690000-30693000	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
7	chr6:30690000-30694000	Transcr. at gene 5' and 3'	Brain Germinal Matrix	brain
8	chr6:30690000-30709600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr6:30690200-30693000	Transcr. at gene 5' and 3'	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr6:30690200-30693400	Transcr. at gene 5' and 3'	NH-A	brain
11	chr6:30690200-30694000	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
12	chr6:30690200-30699200	Strong transcription	Sigmoid Colon	Sigmoid Colon
13	chr6:30690400-30693000	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
14	chr6:30690400-30693200	Transcr. at gene 5' and 3'	Fetal Brain Female	brain
15	chr6:30690400-30696400	Strong transcription	Gastric	stomach
16	chr6:30690400-30709200	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr6:30690600-30692600	Genic enhancers	Cortex derived primary cultured neurospheres	brain
18	chr6:30690600-30692600	Genic enhancers	Colon Smooth Muscle	Colon
19	chr6:30690600-30692800	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
20	chr6:30690600-30693000	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr6:30690600-30693000	Genic enhancers	Liver	Liver
22	chr6:30690600-30693200	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr6:30690600-30693400	Genic enhancers	Fetal Stomach	stomach
24	chr6:30690600-30693600	Weak transcription	Right Atrium	heart
25	chr6:30690600-30693800	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
26	chr6:30690600-30694000	Genic enhancers	Primary T helper cells PMA-I stimulated	--
27	chr6:30690600-30694000	Genic enhancers	Primary T killer naive cells fromperipheralblood	blood
28	chr6:30690600-30694000	Genic enhancers	Adipose Nuclei	Adipose
29	chr6:30690600-30694000	Genic enhancers	Skeletal Muscle Female	skeletal muscle
30	chr6:30690600-30694200	Genic enhancers	Primary T helper cells fromperipheralblood	blood
31	chr6:30690600-30694200	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
32	chr6:30690600-30694400	Genic enhancers	Primary T cells fromperipheralblood	blood
33	chr6:30690600-30694400	Strong transcription	Brain Inferior Temporal Lobe	brain
34	chr6:30690600-30694400	Genic enhancers	Fetal Muscle Leg	muscle
35	chr6:30690600-30694600	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr6:30690600-30698000	Strong transcription	Rectal Mucosa Donor 31	rectum
37	chr6:30690600-30698200	Strong transcription	Left Ventricle	heart
38	chr6:30690600-30698400	Strong transcription	Right Ventricle	heart
39	chr6:30690600-30701200	Strong transcription	Brain Angular Gyrus	brain
40	chr6:30690600-30703800	Strong transcription	Lung	lung
41	chr6:30690800-30693800	Strong transcription	H9 Cell Line	embryonic stem cell
42	chr6:30690800-30693800	Genic enhancers	Stomach Smooth Muscle	stomach
43	chr6:30690800-30694200	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr6:30690800-30694200	Strong transcription	Small Intestine	intestine
45	chr6:30691000-30692600	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr6:30691000-30692600	Strong transcription	Primary B cells from peripheral blood	blood
47	chr6:30691000-30692600	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
48	chr6:30691000-30693000	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr6:30691000-30693200	Strong transcription	ES-I3 Cell Line	embryonic stem cell
50	chr6:30691000-30693600	Strong transcription	Rectal Smooth Muscle	rectum

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