Variant report

Variant	rs6697273
Chromosome Location	chr1:62486381-62486382
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 52 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs1123777	0.84[MEX][hapmap];0.83[AMR][1000 genomes]
rs11577828	1.00[CHB][hapmap]
rs11581307	1.00[CHB][hapmap]
rs11584978	0.84[EUR][1000 genomes]
rs11590158	0.84[ASW][hapmap];0.93[MKK][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11590485	1.00[CHB][hapmap]
rs11590812	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs11590954	1.00[CHB][hapmap]
rs12076492	0.82[TSI][hapmap];0.84[EUR][1000 genomes]
rs1332631	1.00[CHB][hapmap]
rs1412620	1.00[CHB][hapmap]
rs1537316	0.84[EUR][1000 genomes]
rs1537317	0.81[EUR][1000 genomes]
rs17122925	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17122938	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17123017	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2067881	1.00[CHB][hapmap]
rs2067882	1.00[CHB][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2365985	1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];0.86[TSI][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2476180	1.00[CHB][hapmap]
rs34050378	0.81[EUR][1000 genomes]
rs3762449	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[TSI][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41394744	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[TSI][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4325166	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs4915792	0.81[EUR][1000 genomes]
rs4915793	0.81[EUR][1000 genomes]
rs59354521	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61313871	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61775625	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs61775627	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61775628	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61775631	0.84[EUR][1000 genomes]
rs61775652	0.81[EUR][1000 genomes]
rs61775653	0.81[EUR][1000 genomes]
rs61775654	0.81[EUR][1000 genomes]
rs61775655	0.81[EUR][1000 genomes]
rs61775656	0.81[EUR][1000 genomes]
rs61775657	0.81[EUR][1000 genomes]
rs6660262	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6660358	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6695442	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7528431	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs7528797	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7531027	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs7534748	1.00[AMR][1000 genomes];0.95[EUR][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	nsv518627	chr1:62279594-62517947	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv522020	chr1:62279594-62517947	Active TSS ZNF genes & repeats Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv531876	chr1:62302313-62504349	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
4	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
5	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
6	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
7	nsv546416	chr1:62437872-62492215	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6697273	INADL	cis	cerebellum	SCAN

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:62385000-62494200	Weak transcription	Aorta	Aorta
2	chr1:62409200-62518600	Weak transcription	Pancreas	Pancrea
3	chr1:62424200-62494200	Weak transcription	Esophagus	oesophagus
4	chr1:62446600-62487600	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr1:62458800-62521400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
6	chr1:62459000-62516000	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr1:62459000-62530600	Weak transcription	Primary T helper cells PMA-I stimulated	--
8	chr1:62459200-62487800	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr1:62459200-62511200	Weak transcription	Gastric	stomach
10	chr1:62459200-62550000	Weak transcription	Primary T cells fromperipheralblood	blood
11	chr1:62459400-62493800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr1:62459600-62494200	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr1:62460000-62499600	Weak transcription	Fetal Intestine Large	intestine
14	chr1:62460000-62516400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr1:62460000-62544600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
16	chr1:62460200-62487600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr1:62460200-62516000	Weak transcription	HMEC	breast
18	chr1:62466400-62494200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr1:62469000-62533600	Weak transcription	Rectal Smooth Muscle	rectum
20	chr1:62469800-62488000	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr1:62473000-62488200	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr1:62473800-62487000	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr1:62474200-62518600	Weak transcription	Primary T cells from cord blood	blood
24	chr1:62479000-62487600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr1:62479400-62488200	Weak transcription	Psoas Muscle	Psoas
26	chr1:62479400-62490200	Weak transcription	Left Ventricle	heart
27	chr1:62479400-62490200	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr1:62479400-62493600	Weak transcription	Stomach Smooth Muscle	stomach
29	chr1:62479400-62496000	Weak transcription	Fetal Kidney	kidney
30	chr1:62479600-62488000	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr1:62480600-62513000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
32	chr1:62482800-62488000	Weak transcription	Pancreatic Islets	Pancreatic Islet
33	chr1:62483400-62488400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
34	chr1:62484400-62492800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr1:62484400-62523000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr1:62484400-62562200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
37	chr1:62484600-62492400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr1:62484600-62493800	Weak transcription	Duodenum Mucosa	Duodenum
39	chr1:62484600-62494400	Weak transcription	Liver	Liver
40	chr1:62484600-62506000	Weak transcription	NHEK	skin
41	chr1:62484800-62511200	Weak transcription	Rectal Mucosa Donor 31	rectum
42	chr1:62485000-62494000	Weak transcription	Fetal Intestine Small	intestine
43	chr1:62485200-62487600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
44	chr1:62485600-62488400	Strong transcription	Ovary	ovary
45	chr1:62486000-62492600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr1:62486200-62517600	Weak transcription	Primary T helper cells fromperipheralblood	blood

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