Variant report

Variant	rs10494955
Chromosome Location	chr1:212971978-212971979
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:212967045..212969925-chr1:212970724..212972382,2	K562	blood:
2	chr1:212963881..212969695-chr1:212970420..212976060,10	K562	blood:

Variant related genes	Relation type
ENSG00000117697	Chromatin interaction
ENSG00000203705	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs1054733	0.85[ASN][1000 genomes]
rs10863990	0.91[ASN][1000 genomes]
rs10863993	0.96[ASN][1000 genomes]
rs10863995	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10863998	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10863999	0.99[ASN][1000 genomes]
rs10864000	0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs10864001	0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs11120011	0.93[ASN][1000 genomes]
rs11120012	0.94[ASN][1000 genomes]
rs11120013	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11120019	0.93[ASN][1000 genomes]
rs11120024	0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs11120025	0.85[CHB][hapmap];0.83[JPT][hapmap];0.90[ASN][1000 genomes]
rs11120026	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11120027	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11120032	0.88[ASN][1000 genomes]
rs11120037	0.86[ASN][1000 genomes]
rs11120039	0.84[ASN][1000 genomes]
rs1133462	0.90[ASN][1000 genomes]
rs12064985	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12088916	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12095846	0.86[ASN][1000 genomes]
rs12097897	0.91[JPT][hapmap];0.99[ASN][1000 genomes]
rs12125321	0.89[ASN][1000 genomes]
rs12126017	0.99[ASN][1000 genomes]
rs12130945	0.90[ASN][1000 genomes]
rs12132316	0.95[ASN][1000 genomes]
rs12136046	0.96[ASN][1000 genomes]
rs12136834	0.96[ASN][1000 genomes]
rs12565557	0.83[ASN][1000 genomes]
rs12722742	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12734406	0.81[ASN][1000 genomes]
rs12734543	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12737398	0.90[ASN][1000 genomes]
rs12741704	0.96[ASN][1000 genomes]
rs12743402	0.91[ASN][1000 genomes]
rs12744602	0.86[ASN][1000 genomes]
rs12747251	0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs12759287	0.83[ASN][1000 genomes]
rs2359322	0.90[ASN][1000 genomes]
rs34274815	0.81[ASN][1000 genomes]
rs3820679	0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs3862953	0.90[ASN][1000 genomes]
rs4951457	0.85[CEU][hapmap]
rs4951460	0.81[EUR][1000 genomes]
rs4951463	0.96[ASN][1000 genomes]
rs4951638	1.00[AFR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61829243	0.86[ASN][1000 genomes]
rs6540761	0.87[ASN][1000 genomes]
rs6540763	0.94[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs6661720	0.96[ASN][1000 genomes]
rs6669492	0.88[ASN][1000 genomes]
rs6679350	0.96[ASN][1000 genomes]
rs6679549	0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs6689604	1.00[CHB][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs6690689	0.96[ASN][1000 genomes]
rs6693311	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6694452	0.89[ASN][1000 genomes]
rs6697507	0.85[ASN][1000 genomes]
rs6700410	0.95[CHB][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs6702025	0.89[ASN][1000 genomes]
rs6702611	0.99[ASN][1000 genomes]
rs7554105	0.90[ASN][1000 genomes]
rs7556272	0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001637	chr1:212907611-213034606	Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
2	esv2756884	chr1:212925429-213006397	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
3	esv2758997	chr1:212925429-213006397	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
4	nsv1010003	chr1:212944240-212986996	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs10494955	LQK1	cis	lesional skin	skin_eQTL
rs10494955	FLVCR1-AS1	cis	Adipose Subcutaneous	GTEx
rs10494955	FLVCR1-AS1	cis	Skin Sun Exposed Lower leg	GTEx
rs10494955	LQK1	Cis_1M	lymphoblastoid	RTeQTL
rs10494955	FLVCR1-AS1	cis	Esophagus Muscularis	GTEx
rs10494955	FLVCR1-AS1	cis	Nerve Tibial	GTEx
rs10494955	FLVCR1-AS1	cis	Artery Aorta	GTEx
rs10494955	LQK1	cis	uninvolved skin	skin_eQTL

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212965800-212972000	Weak transcription	Gastric	stomach
2	chr1:212965800-212992600	Weak transcription	Lung	lung
3	chr1:212966000-212972000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr1:212966000-212974800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr1:212966000-212981200	Weak transcription	Esophagus	oesophagus
6	chr1:212966000-212983000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr1:212966000-212997400	Weak transcription	Aorta	Aorta
8	chr1:212966200-212972000	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr1:212966200-212973800	Weak transcription	Colonic Mucosa	Colon
10	chr1:212966200-212975600	Weak transcription	HMEC	breast
11	chr1:212966200-212979800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr1:212966400-212972000	Weak transcription	Fetal Brain Female	brain
13	chr1:212966400-212972000	Weak transcription	Fetal Muscle Leg	muscle
14	chr1:212966400-212972000	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr1:212966400-212972000	Weak transcription	Thymus	Thymus
16	chr1:212966400-212977400	Weak transcription	Hela-S3	cervix
17	chr1:212966400-212984000	Weak transcription	Rectal Smooth Muscle	rectum
18	chr1:212966400-212985600	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr1:212966400-212988200	Weak transcription	Fetal Heart	heart
20	chr1:212966400-212989600	Weak transcription	Fetal Brain Male	brain
21	chr1:212966400-212990200	Weak transcription	Right Ventricle	heart
22	chr1:212966800-212977600	Weak transcription	Brain Germinal Matrix	brain
23	chr1:212966800-212989600	Weak transcription	Psoas Muscle	Psoas
24	chr1:212967000-212972000	Weak transcription	NHEK	skin
25	chr1:212967000-212979000	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr1:212967000-212984400	Weak transcription	Spleen	Spleen
27	chr1:212967200-212975400	Weak transcription	HSMM	muscle
28	chr1:212967200-212984000	Weak transcription	NHDF-Ad	bronchial
29	chr1:212967200-212988400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr1:212967200-212989000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr1:212967200-212989600	Weak transcription	NHLF	lung
32	chr1:212968000-212980000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr1:212968000-212987400	Weak transcription	Fetal Intestine Large	intestine
34	chr1:212968200-212972000	Weak transcription	Fetal Intestine Small	intestine
35	chr1:212968400-212972000	Weak transcription	Brain Cingulate Gyrus	brain
36	chr1:212968400-212972000	Weak transcription	Brain Substantia Nigra	brain
37	chr1:212968400-212974400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
38	chr1:212968400-212988000	Weak transcription	Stomach Mucosa	stomach
39	chr1:212968600-212972400	Strong transcription	K562	blood
40	chr1:212968600-212980200	Weak transcription	HUVEC	blood vessel
41	chr1:212968800-212974600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr1:212969000-212972000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr1:212969000-212972400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
44	chr1:212969000-212972400	Strong transcription	Duodenum Smooth Muscle	Duodenum
45	chr1:212969000-212972600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr1:212969000-212973400	Strong transcription	Primary T cells fromperipheralblood	blood
47	chr1:212969000-212973800	Strong transcription	HUES64 Cell Line	embryonic stem cell
48	chr1:212969000-212975400	Strong transcription	HUES48 Cell Line	embryonic stem cell
49	chr1:212969000-212976200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr1:212969000-212976400	Strong transcription	Liver	Liver

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