Variant report

Variant	rs6688017
Chromosome Location	chr1:62575911-62575912
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	MAFK	chr1:62575901-62576199	HepG2	liver:	n/a	chr1:62576079-62576090 chr1:62576075-62576091 chr1:62576075-62576090

Variant related genes	Relation type
INADL	TF binding region

Extended variants
information (count: 25 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10127438	0.90[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.86[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11207901	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1964872	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2025290	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4255414	0.90[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.83[TSI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4915796	0.85[CEU][hapmap];0.88[AMR][1000 genomes]
rs4915797	0.85[CEU][hapmap];0.86[MEX][hapmap];0.88[AMR][1000 genomes]
rs56777178	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs58323203	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58585691	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59295242	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61777670	0.88[EUR][1000 genomes]
rs61777684	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs61777691	0.83[AMR][1000 genomes]
rs6684468	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6700644	0.93[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.85[YRI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7512777	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7531424	0.83[AMR][1000 genomes]
rs7535670	0.90[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7537716	0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1004446	chr1:62394631-62813533	Enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
2	nsv534984	chr1:62394631-62813533	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
3	nsv1001667	chr1:62407786-62649838	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
4	nsv461650	chr1:62542717-62657530	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
5	nsv546417	chr1:62542717-62657530	Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6688017	ROR1	cis	cerebellum	SCAN
rs6688017	INADL	cis	cerebellum	SCAN

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:62508200-62628400	Weak transcription	Colonic Mucosa	Colon
2	chr1:62532600-62587600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr1:62536200-62619400	Weak transcription	Rectal Smooth Muscle	rectum
4	chr1:62542400-62586800	Weak transcription	NHEK	skin
5	chr1:62542400-62587400	Weak transcription	HMEC	breast
6	chr1:62545400-62606800	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr1:62548200-62594000	Weak transcription	Stomach Smooth Muscle	stomach
8	chr1:62548400-62629800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr1:62550200-62607800	Weak transcription	Right Ventricle	heart
10	chr1:62551400-62576000	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr1:62551800-62594200	Weak transcription	Primary T cells fromperipheralblood	blood
12	chr1:62551800-62614000	Weak transcription	Primary T cells from cord blood	blood
13	chr1:62553000-62579000	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr1:62553000-62582800	Weak transcription	Primary T helper cells PMA-I stimulated	--
15	chr1:62553200-62594200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr1:62553400-62579600	Weak transcription	Pancreas	Pancrea
17	chr1:62553600-62579600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr1:62554200-62614000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr1:62554400-62581600	Weak transcription	Duodenum Mucosa	Duodenum
20	chr1:62555000-62589800	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr1:62555000-62594200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr1:62556000-62594200	Weak transcription	Left Ventricle	heart
23	chr1:62559600-62582000	Weak transcription	Liver	Liver
24	chr1:62563400-62576000	Weak transcription	Psoas Muscle	Psoas
25	chr1:62563600-62617400	Weak transcription	Brain Anterior Caudate	brain
26	chr1:62566000-62593600	Weak transcription	Primary T helper cells fromperipheralblood	blood
27	chr1:62566200-62579600	Weak transcription	Gastric	stomach
28	chr1:62566200-62582200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr1:62566200-62594400	Weak transcription	Aorta	Aorta
30	chr1:62566200-62603400	Weak transcription	Esophagus	oesophagus
31	chr1:62566200-62604400	Weak transcription	Lung	lung
32	chr1:62566200-62614000	Weak transcription	Adipose Nuclei	Adipose
33	chr1:62566400-62578000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr1:62566600-62577800	Weak transcription	Fetal Intestine Small	intestine
35	chr1:62566800-62608000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr1:62567200-62594200	Weak transcription	Rectal Mucosa Donor 31	rectum
37	chr1:62569800-62594400	Weak transcription	H1 Cell Line	embryonic stem cell
38	chr1:62570000-62594400	Weak transcription	HUES48 Cell Line	embryonic stem cell
39	chr1:62570200-62576800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
40	chr1:62570200-62607800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
41	chr1:62572600-62578000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr1:62574800-62576200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr1:62574800-62576600	Enhancers	Ovary	ovary
44	chr1:62574800-62577200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr1:62575000-62587200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
46	chr1:62575200-62608000	Weak transcription	Fetal Kidney	kidney
47	chr1:62575800-62576200	Enhancers	HSMMtube	muscle
48	chr1:62575800-62576600	Strong transcription	Fetal Intestine Large	intestine
49	chr1:62575800-62576600	Enhancers	Skeletal Muscle Female	skeletal muscle

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