Variant report

Variant	rs7947357
Chromosome Location	chr11:57414387-57414388
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:59)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:59 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ATF2	chr11:57413960-57416168	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr11:57414171-57414818	HUVEC	blood vessel:	n/a	n/a
3	POLR2A	chr11:57411937-57420676	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr11:57410796-57421100	H1-hESC	embryonic stem cell:	n/a	n/a
5	PBX3	chr11:57414093-57418151	SK-N-SH	brain:	n/a	chr11:57415576-57415585
6	POLR2A	chr11:57414127-57415510	HepG2	liver:	n/a	n/a
7	POLR2A	chr11:57412052-57419760	MCF10A-Er-Src	breast:	n/a	n/a
8	POLR2A	chr11:57404829-57418710	PFSK-1	brain:	n/a	n/a
9	TEAD4	chr11:57414272-57414749	H1-hESC	embryonic stem cell:	n/a	n/a
10	POLR2A	chr11:57410821-57420904	H1-hESC	embryonic stem cell:	n/a	n/a
11	POLR2A	chr11:57412821-57416389	HUVEC	blood vessel:	n/a	n/a
12	POLR2A	chr11:57414281-57414717	A549	lung:	n/a	n/a
13	SIN3A	chr11:57413866-57417706	H1-hESC	embryonic stem cell:	n/a	chr11:57414716-57414729 chr11:57416870-57416883 chr11:57415091-57415101 chr11:57417329-57417340
14	POLR2A	chr11:57413864-57414896	HepG2	liver:	n/a	n/a
15	POLR2A	chr11:57411926-57416336	HUVEC	blood vessel:	n/a	n/a
16	POLR2A	chr11:57411980-57417263	H1-hESC	embryonic stem cell:	n/a	n/a
17	POLR2A	chr11:57414164-57415210	A549	lung:	n/a	n/a
18	POLR2A	chr11:57414138-57417886	ProgFib	skin:	n/a	n/a
19	POLR2A	chr11:57414165-57414727	A549	lung:	n/a	n/a
20	USF2	chr11:57414128-57417940	H1-hESC	embryonic stem cell:	n/a	n/a
21	GTF2F1	chr11:57414056-57414514	H1-hESC	embryonic stem cell:	n/a	n/a
22	POLR2A	chr11:57414033-57415179	H1-hESC	embryonic stem cell:	n/a	n/a
23	POLR2A	chr11:57404802-57417187	SK-N-MC	brain:	n/a	n/a
24	POLR2A	chr11:57412040-57416702	SK-N-MC	brain:	n/a	n/a
25	POLR2A	chr11:57411922-57418069	SK-N-SH	brain:	n/a	n/a
26	POLR2A	chr11:57414387-57414696	HepG2	liver:	n/a	n/a
27	NANOG	chr11:57414184-57415143	H1-hESC	embryonic stem cell:	n/a	n/a
28	SP4	chr11:57414155-57415248	H1-hESC	embryonic stem cell:	n/a	n/a
29	BCL3	chr11:57414053-57414671	A549	lung:	n/a	n/a
30	CHD2	chr11:57413968-57418190	H1-hESC	embryonic stem cell:	n/a	n/a
31	JUND	chr11:57414217-57414783	H1-hESC	embryonic stem cell:	n/a	n/a
32	POLR2A	chr11:57412961-57418210	MCF10A-Er-Src	breast:	n/a	n/a
33	CREB1	chr11:57414154-57415328	H1-hESC	embryonic stem cell:	n/a	n/a
34	PBX3	chr11:57414226-57416231	A549	lung:	n/a	chr11:57415576-57415585
35	PBX3	chr11:57414362-57416288	A549	lung:	n/a	chr11:57415576-57415585
36	POLR2A	chr11:57414233-57414776	HCT-116	colon:	n/a	n/a
37	POLR2A	chr11:57413929-57416256	HUVEC	blood vessel:	n/a	n/a
38	TAF7	chr11:57414171-57415375	H1-hESC	embryonic stem cell:	n/a	n/a
39	POLR2A	chr11:57412201-57418679	ECC-1	luminal epithelium:	n/a	n/a
40	POLR2A	chr11:57413511-57415806	PANC-1	pancreas:	n/a	n/a
41	POLR2A	chr11:57414249-57414645	HepG2	liver:	n/a	n/a
42	PBX3	chr11:57414325-57415153	SK-N-SH	brain:	n/a	n/a
43	POLR2A	chr11:57410100-57417938	PBDE	blood:	n/a	n/a
44	NRF1	chr11:57414336-57414705	H1-hESC	embryonic stem cell:	n/a	n/a
45	POLR2A	chr11:57414093-57415283	SK-N-SH	brain:	n/a	n/a
46	POLR2A	chr11:57414193-57418271	A549	lung:	n/a	n/a
47	POLR2A	chr11:57414036-57415597	U87	brain:	n/a	n/a
48	POLR2A	chr11:57414059-57414756	H1-neurons	neurons:	n/a	n/a
49	POLR2A	chr11:57413874-57415297	HUVEC	blood vessel:	n/a	n/a
50	POLR2A	chr11:57414145-57414398	HepG2	liver:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:57224684..57228396-chr11:57412206..57415806,3	K562	blood:
2	chr11:57335649..57336286-chr11:57413903..57414633,2	MCF-7	breast:
3	chr11:57191864..57193854-chr11:57413705..57415355,2	K562	blood:
4	chr11:57411538..57415148-chr11:57422707..57424942,3	K562	blood:
5	chr11:57191864..57194047-chr11:57412922..57415205,2	K562	blood:
6	chr11:57333866..57335515-chr11:57412954..57415220,2	MCF-7	breast:
7	chr11:57414343..57418921-chr11:57423216..57427343,7	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZDHHC5-1	chr11:57414359-57414493	ENSG00000254602.1

No data

Variant related genes	Relation type
ENSG00000254602	TF binding region
CLP1	TF binding region
ENSG00000186907	Chromatin interaction
ENSG00000134802	Chromatin interaction
ENSG00000172409	Chromatin interaction
ENSG00000156587	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10792110	1.00[JPT][hapmap]
rs10896644	1.00[JPT][hapmap]
rs10896649	1.00[JPT][hapmap]
rs11229109	1.00[JPT][hapmap]
rs11570176	1.00[JPT][hapmap]
rs11570181	1.00[JPT][hapmap]
rs1613592	0.84[CEU][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.80[TSI][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1631684	0.81[CEU][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1647394	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1647403	0.88[JPT][hapmap];0.84[EUR][1000 genomes]
rs17455422	1.00[JPT][hapmap]
rs1783826	0.89[CEU][hapmap];1.00[JPT][hapmap]
rs1783827	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1783828	1.00[CEU][hapmap];0.93[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1783829	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1783978	1.00[JPT][hapmap]
rs1783979	1.00[JPT][hapmap]
rs1783980	1.00[JPT][hapmap]
rs1783981	1.00[JPT][hapmap]
rs1783983	0.84[CEU][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.80[TSI][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1783985	0.83[EUR][1000 genomes]
rs1785498	1.00[JPT][hapmap]
rs1798172	0.84[CEU][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.80[TSI][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1798173	0.81[CEU][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.81[EUR][1000 genomes]
rs1798177	1.00[CEU][hapmap];0.93[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2156638	1.00[JPT][hapmap]
rs2956981	1.00[JPT][hapmap]
rs3017889	1.00[JPT][hapmap]
rs36036499	1.00[JPT][hapmap]
rs4611222	1.00[JPT][hapmap]
rs627145	1.00[JPT][hapmap]
rs653889	1.00[JPT][hapmap]
rs665058	1.00[JPT][hapmap]
rs7117020	1.00[JPT][hapmap]
rs7120868	1.00[JPT][hapmap]
rs929934	1.00[CEU][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1044030	chr11:57073395-58035564	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
2	nsv541047	chr11:57073395-58035564	Active TSS Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
3	nsv530621	chr11:57139699-57703639	Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Weak 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	109 gene(s)	inside rSNPs	diseases
4	nsv832163	chr11:57299354-57481050	Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
5	nsv1040913	chr11:57315006-57696122	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
6	nsv832164	chr11:57407617-57578825	Enhancers Strong transcription Genic enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
7	esv992553	chr11:57408294-57419351	Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs7947357	TIMM10	cis	parietal	SCAN
rs7947357	VWCE	cis	cerebellum	SCAN
rs7947357	SLC43A3	cis	cerebellum	SCAN
rs7947357	OR5B17	cis	parietal	SCAN
rs7947357	CD5	cis	parietal	SCAN
rs7947357	YPEL4	cis	lymphoblastoid	seeQTL
rs7947357	TIMM10	Cis_1M	lymphoblastoid	RTeQTL
rs7947357	YPEL4	cis	lung	GTEx
rs7947357	MS4A7	cis	parietal	SCAN
rs7947357	TNKS1BP1	cis	parietal	SCAN

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:57409000-57414400	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr11:57409000-57416200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr11:57411000-57414600	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
4	chr11:57411200-57414800	Enhancers	ES-I3 Cell Line	embryonic stem cell
5	chr11:57411200-57414800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr11:57411200-57415600	Enhancers	K562	blood
7	chr11:57411600-57416200	Enhancers	Fetal Lung	lung
8	chr11:57412000-57414400	Enhancers	Brain Anterior Caudate	brain
9	chr11:57412000-57414400	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
10	chr11:57412000-57415800	Enhancers	Placenta Amnion	Placenta Amnion
11	chr11:57412200-57414400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr11:57412200-57414400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr11:57412200-57414800	Bivalent Enhancer	Rectal Mucosa Donor 29	rectum
14	chr11:57412200-57414800	Enhancers	HSMMtube	muscle
15	chr11:57412200-57415800	Enhancers	Ovary	ovary
16	chr11:57412200-57416200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr11:57412200-57416400	Bivalent Enhancer	Fetal Intestine Large	intestine
18	chr11:57412200-57416800	Enhancers	Lung	lung
19	chr11:57412200-57416800	Enhancers	Spleen	Spleen
20	chr11:57412200-57417000	Bivalent Enhancer	Stomach Mucosa	stomach
21	chr11:57412400-57414400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
22	chr11:57412600-57414400	Enhancers	HUES48 Cell Line	embryonic stem cell
23	chr11:57412800-57416000	Bivalent Enhancer	Fetal Thymus	thymus
24	chr11:57413000-57414400	Bivalent Enhancer	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr11:57413000-57414600	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr11:57413000-57415000	Bivalent Enhancer	Duodenum Mucosa	Duodenum
27	chr11:57413000-57415800	Enhancers	Fetal Brain Male	brain
28	chr11:57413000-57415800	Bivalent Enhancer	Rectal Smooth Muscle	rectum
29	chr11:57413000-57416400	Enhancers	Right Ventricle	heart
30	chr11:57413000-57416800	Bivalent Enhancer	NH-A	brain
31	chr11:57413200-57414800	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
32	chr11:57413200-57414800	Bivalent Enhancer	Stomach Smooth Muscle	stomach
33	chr11:57413200-57416000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr11:57413200-57416200	Bivalent Enhancer	NHLF	lung
35	chr11:57413200-57416600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr11:57413200-57417400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr11:57413400-57414400	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
38	chr11:57413400-57414400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr11:57413400-57414400	Weak transcription	HSMM	muscle
40	chr11:57413400-57414400	Bivalent Enhancer	NHEK	skin
41	chr11:57413400-57414800	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr11:57413400-57415000	Enhancers	Fetal Heart	heart
43	chr11:57413400-57415800	Bivalent Enhancer	Adipose Nuclei	Adipose
44	chr11:57413400-57416000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
45	chr11:57413400-57416000	Bivalent Enhancer	Fetal Stomach	stomach
46	chr11:57413400-57416000	Bivalent Enhancer	Dnd41	blood
47	chr11:57413400-57416200	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
48	chr11:57413400-57416600	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
49	chr11:57413600-57414400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
50	chr11:57413600-57414400	Genic enhancers	Brain Cingulate Gyrus	brain

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