Variant report

Variant	rs6665822
Chromosome Location	chr1:155103147-155103148
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:10)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:10 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:155097222-155104778	HepG2	liver:	n/a	n/a
2	POLR2A	chr1:155101017-155103272	HepG2	liver:	n/a	n/a
3	POLR2A	chr1:155100249-155104737	HepG2	liver:	n/a	n/a
4	POLR2A	chr1:155102980-155103192	HepG2	liver:	n/a	n/a
5	HEY1	chr1:155096801-155104706	HepG2	liver:	n/a	n/a
6	MXI1	chr1:155099180-155103687	SK-N-SH	brain:	n/a	n/a
7	POLR2A	chr1:155102936-155103430	HUVEC	blood vessel:	n/a	n/a
8	TAL1	chr1:155102912-155103186	K562	blood:	n/a	chr1:155103058-155103076
9	POLR2A	chr1:155100252-155104734	HepG2	liver:	n/a	n/a
10	POLR2A	chr1:155098646-155104670	HUVEC	blood vessel:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:154973069..154975738-chr1:155098828..155103753,6	MCF-7	breast:
2	chr1:155094769..155105017-chr1:155135344..155151845,46	MCF-7	breast:
3	chr1:155049589..155073019-chr1:155085330..155115362,149	MCF-7	breast:
4	chr1:155095314..155110392-chr1:155134312..155151496,72	MCF-7	breast:
5	chr1:154971203..154978007-chr1:155093683..155103687,24	MCF-7	breast:
6	chr1:155102095..155105261-chr1:155144437..155147447,3	K562	blood:
7	chr1:154942779..154946822-chr1:155099948..155103477,6	MCF-7	breast:
8	chr1:155096309..155104200-chr1:155157595..155166389,23	MCF-7	breast:
9	chr1:155022054..155026411-chr1:155097710..155103379,8	MCF-7	breast:

No data

Variant related genes	Relation type
EFNA1	TF binding region
SLC50A1	TF binding region
ENSG00000143537	Chromatin interaction
ENSG00000160685	Chromatin interaction
ENSG00000271748	Chromatin interaction
ENSG00000273088	Chromatin interaction
ENSG00000163463	Chromatin interaction
ENSG00000185499	Chromatin interaction
ENSG00000160691	Chromatin interaction
ENSG00000163462	Chromatin interaction
ENSG00000169231	Chromatin interaction
ENSG00000143590	Chromatin interaction

Extended variants
information (count: 80 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs1001848	1.00[JPT][hapmap]
rs10157801	0.85[JPT][hapmap]
rs10796938	0.93[ASN][1000 genomes]
rs10796939	0.93[ASN][1000 genomes]
rs10908454	1.00[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs10908455	1.00[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs10908456	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs10908458	0.85[JPT][hapmap]
rs11264304	0.85[JPT][hapmap]
rs11264306	1.00[JPT][hapmap]
rs11264312	0.93[ASN][1000 genomes]
rs11264313	0.90[ASN][1000 genomes]
rs11264314	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs11264319	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs11264321	0.93[ASN][1000 genomes]
rs11264322	0.95[ASN][1000 genomes]
rs11264327	1.00[ASN][1000 genomes]
rs11264328	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11264329	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.90[MKK][hapmap];0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11264337	0.80[GIH][hapmap]
rs11264338	0.80[GIH][hapmap]
rs11264339	0.80[GIH][hapmap]
rs12025371	0.85[JPT][hapmap]
rs12026113	0.95[ASN][1000 genomes]
rs12028043	0.85[JPT][hapmap]
rs12039316	0.93[ASN][1000 genomes]
rs12040970	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.90[MKK][hapmap];0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12145362	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12904	0.85[JPT][hapmap]
rs1462855	1.00[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs1870939	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2306124	1.00[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs34815285	0.85[ASN][1000 genomes]
rs35902694	0.85[JPT][hapmap]
rs3765087	1.00[JPT][hapmap]
rs3766916	1.00[JPT][hapmap]
rs3766918	0.93[ASN][1000 genomes]
rs3806256	0.85[JPT][hapmap]
rs4045192	0.85[JPT][hapmap]
rs4246529	0.85[JPT][hapmap]
rs4276913	0.85[JPT][hapmap]
rs4303067	0.88[ASN][1000 genomes]
rs4361977	0.93[ASN][1000 genomes]
rs4421576	0.80[GIH][hapmap]
rs4460629	0.80[GIH][hapmap]
rs4625273	0.93[ASN][1000 genomes]
rs4745	0.82[GIH][hapmap];0.85[JPT][hapmap]
rs4845407	1.00[JPT][hapmap]
rs4845408	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4971052	1.00[JPT][hapmap]
rs4971066	0.85[JPT][hapmap]
rs4971073	0.85[JPT][hapmap]
rs4971076	0.85[JPT][hapmap]
rs4971079	0.80[GIH][hapmap];0.85[JPT][hapmap]
rs56112907	0.93[ASN][1000 genomes]
rs6427158	1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs6693477	1.00[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs7364524	0.85[JPT][hapmap]
rs7364869	0.93[ASN][1000 genomes]
rs7365544	1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs7366138	0.98[ASN][1000 genomes]
rs7366355	0.93[ASN][1000 genomes]
rs7367207	1.00[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs7367758	0.95[ASN][1000 genomes]
rs7367897	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs7368345	1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs7534162	1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs7548955	1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs7556304	0.80[GIH][hapmap]
rs9297	0.85[JPT][hapmap]
rs9330263	0.80[AMR][1000 genomes];0.95[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	nsv532579	chr1:154548165-155262692	Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Weak transcription Genic enhancers Bivalent Enhancer 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	575 gene(s)	inside rSNPs	diseases
2	esv1823746	chr1:154965207-155231904	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer 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	469 gene(s)	inside rSNPs	diseases
3	nsv872455	chr1:155003954-155106550	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
4	nsv998756	chr1:155080090-155136545	Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
5	nsv464084	chr1:155082298-155194980	Weak transcription Bivalent Enhancer Active TSS Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	366 gene(s)	inside rSNPs	diseases
6	nsv547961	chr1:155082298-155194980	Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	366 gene(s)	inside rSNPs	diseases
7	nsv831614	chr1:155094978-155275031	Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer 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	434 gene(s)	inside rSNPs	diseases
8	esv2757756	chr1:155094978-155314807	Bivalent Enhancer Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	452 gene(s)	inside rSNPs	diseases
9	esv2758971	chr1:155094978-155314807	Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Enhancers 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	452 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs6665822	CRNN	cis	cerebellum	SCAN
rs6665822	RPRD2	cis	parietal	SCAN
rs6665822	SPRR4	cis	parietal	SCAN
rs6665822	SMCP	cis	cerebellum	SCAN
rs6665822	GBAP1	cis	Artery Tibial	GTEx
rs6665822	S100A3	cis	parietal	SCAN
rs6665822	LASS2	cis	parietal	SCAN

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:155098400-155103200	Active TSS	Liver	Liver
2	chr1:155098800-155103400	Active TSS	Pancreatic Islets	Pancreatic Islet
3	chr1:155099200-155103200	Active TSS	Small Intestine	intestine
4	chr1:155099600-155103600	Active TSS	Left Ventricle	heart
5	chr1:155099800-155103600	Active TSS	Lung	lung
6	chr1:155100000-155103400	Active TSS	Esophagus	oesophagus
7	chr1:155100400-155103200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr1:155100400-155103400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr1:155100400-155103400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
10	chr1:155100600-155103200	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
11	chr1:155100800-155103200	Flanking Active TSS	NHEK	skin
12	chr1:155100800-155103400	Flanking Active TSS	Fetal Heart	heart
13	chr1:155100800-155103400	Flanking Active TSS	HMEC	breast
14	chr1:155100800-155103600	Flanking Active TSS	HUVEC	blood vessel
15	chr1:155100800-155103800	Weak transcription	Aorta	Aorta
16	chr1:155101000-155103400	Flanking Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr1:155101000-155103400	Enhancers	Spleen	Spleen
18	chr1:155101000-155104600	Enhancers	K562	blood
19	chr1:155101200-155103200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr1:155101400-155103200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr1:155101400-155104000	Transcr. at gene 5' and 3'	Fetal Intestine Small	intestine
22	chr1:155101600-155103200	Active TSS	Fetal Intestine Large	intestine
23	chr1:155101600-155103200	Flanking Active TSS	Stomach Smooth Muscle	stomach
24	chr1:155101600-155103400	Active TSS	Fetal Kidney	kidney
25	chr1:155101600-155103800	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr1:155101800-155103800	Active TSS	Rectal Smooth Muscle	rectum
27	chr1:155101800-155104600	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr1:155102000-155103400	Enhancers	Cortex derived primary cultured neurospheres	brain
29	chr1:155102200-155103200	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr1:155102200-155103400	Enhancers	Primary T helper cells PMA-I stimulated	--
31	chr1:155102400-155103200	Enhancers	Primary T cells from cord blood	blood
32	chr1:155102400-155103200	Active TSS	Sigmoid Colon	Sigmoid Colon
33	chr1:155102400-155103400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr1:155102400-155103400	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
35	chr1:155102400-155103400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
36	chr1:155102400-155103600	Active TSS	Rectal Mucosa Donor 29	rectum
37	chr1:155102400-155103600	Active TSS	Right Ventricle	heart
38	chr1:155102400-155103800	Flanking Active TSS	Adipose Nuclei	Adipose
39	chr1:155102400-155106800	Weak transcription	Dnd41	blood
40	chr1:155102400-155107000	Weak transcription	HSMM	muscle
41	chr1:155102400-155107400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
42	chr1:155102400-155107400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
43	chr1:155102600-155103200	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
44	chr1:155102600-155103400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr1:155102600-155103600	Flanking Active TSS	Stomach Mucosa	stomach
46	chr1:155102600-155103800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr1:155102600-155103800	Weak transcription	HSMMtube	muscle
48	chr1:155102600-155107400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
49	chr1:155102800-155103200	Active TSS	HUES6 Cell Line	embryonic stem cell
50	chr1:155102800-155103200	Active TSS	Brain Angular Gyrus	brain

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