Variant report

Variant	rs12097897
Chromosome Location	chr1:212970898-212970899
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:212967045..212969925-chr1:212970724..212972382,2	K562	blood:
2	chr1:212963881..212969695-chr1:212970420..212976060,10	K562	blood:
3	chr1:212873187..212876182-chr1:212968130..212971085,2	K562	blood:

Variant related genes	Relation type
ENSG00000203705	Chromatin interaction
ENSG00000117697	Chromatin interaction
ENSG00000123685	Chromatin interaction

Extended variants
information (count: 72 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10494955	0.91[JPT][hapmap];0.99[ASN][1000 genomes]
rs1054733	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10863990	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10863993	0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10863995	0.90[ASN][1000 genomes]
rs10863998	0.98[ASN][1000 genomes]
rs10863999	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10864000	0.84[CHB][hapmap];0.91[JPT][hapmap];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10864001	0.90[CHB][hapmap];0.95[JPT][hapmap];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11120002	0.90[EUR][1000 genomes]
rs11120011	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11120012	0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11120013	0.95[ASN][1000 genomes]
rs11120019	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11120024	0.90[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11120025	0.81[CHB][hapmap];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11120026	0.96[ASN][1000 genomes]
rs11120027	0.83[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs11120032	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11120037	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11120039	0.85[ASN][1000 genomes]
rs1133462	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12064985	0.95[ASN][1000 genomes]
rs12088916	0.96[ASN][1000 genomes]
rs12095846	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12125321	0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12126017	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12130945	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12132316	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12136046	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12136834	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12565557	0.82[ASN][1000 genomes]
rs12722742	0.96[ASN][1000 genomes]
rs12725274	0.81[EUR][1000 genomes]
rs12727790	0.89[EUR][1000 genomes]
rs12734406	0.81[ASN][1000 genomes]
rs12734543	0.84[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs12737398	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12741704	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12743402	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12744602	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12747251	0.90[CHB][hapmap];0.95[JPT][hapmap];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12759287	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2359322	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34274815	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3820679	0.84[CHB][hapmap];0.91[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3862953	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4951463	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4951636	0.90[EUR][1000 genomes]
rs4951637	0.83[EUR][1000 genomes]
rs4951638	0.95[ASN][1000 genomes]
rs61829243	0.85[ASN][1000 genomes]
rs6540761	0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6540763	0.84[CHB][hapmap];0.91[JPT][hapmap];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6661720	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6669492	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6679350	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6679549	0.84[CHB][hapmap];0.91[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6689604	0.82[JPT][hapmap];0.86[ASN][1000 genomes]
rs6690689	0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6693311	0.96[ASN][1000 genomes]
rs6694452	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6697507	0.86[ASN][1000 genomes]
rs6700410	0.90[CHB][hapmap];0.87[JPT][hapmap];0.86[ASN][1000 genomes]
rs6702025	0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6702611	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7554105	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7556272	0.95[EUR][1000 genomes];0.97[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12097897	LQK1	Cis_1M	lymphoblastoid	RTeQTL
rs12097897	NSL1	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212965800-212971000	Weak transcription	Small Intestine	intestine
2	chr1:212965800-212972000	Weak transcription	Gastric	stomach
3	chr1:212965800-212992600	Weak transcription	Lung	lung
4	chr1:212966000-212972000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr1:212966000-212974800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr1:212966000-212981200	Weak transcription	Esophagus	oesophagus
7	chr1:212966000-212983000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr1:212966000-212997400	Weak transcription	Aorta	Aorta
9	chr1:212966200-212971000	Weak transcription	HSMMtube	muscle
10	chr1:212966200-212971800	Weak transcription	Fetal Kidney	kidney
11	chr1:212966200-212972000	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr1:212966200-212973800	Weak transcription	Colonic Mucosa	Colon
13	chr1:212966200-212975600	Weak transcription	HMEC	breast
14	chr1:212966200-212979800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr1:212966400-212972000	Weak transcription	Fetal Brain Female	brain
16	chr1:212966400-212972000	Weak transcription	Fetal Muscle Leg	muscle
17	chr1:212966400-212972000	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr1:212966400-212972000	Weak transcription	Thymus	Thymus
19	chr1:212966400-212977400	Weak transcription	Hela-S3	cervix
20	chr1:212966400-212984000	Weak transcription	Rectal Smooth Muscle	rectum
21	chr1:212966400-212985600	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr1:212966400-212988200	Weak transcription	Fetal Heart	heart
23	chr1:212966400-212989600	Weak transcription	Fetal Brain Male	brain
24	chr1:212966400-212990200	Weak transcription	Right Ventricle	heart
25	chr1:212966800-212977600	Weak transcription	Brain Germinal Matrix	brain
26	chr1:212966800-212989600	Weak transcription	Psoas Muscle	Psoas
27	chr1:212967000-212972000	Weak transcription	NHEK	skin
28	chr1:212967000-212979000	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr1:212967000-212984400	Weak transcription	Spleen	Spleen
30	chr1:212967200-212975400	Weak transcription	HSMM	muscle
31	chr1:212967200-212984000	Weak transcription	NHDF-Ad	bronchial
32	chr1:212967200-212988400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr1:212967200-212989000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr1:212967200-212989600	Weak transcription	NHLF	lung
35	chr1:212968000-212980000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr1:212968000-212987400	Weak transcription	Fetal Intestine Large	intestine
37	chr1:212968200-212971600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr1:212968200-212972000	Weak transcription	Fetal Intestine Small	intestine
39	chr1:212968400-212971000	Weak transcription	Primary T cells from cord blood	blood
40	chr1:212968400-212972000	Weak transcription	Brain Cingulate Gyrus	brain
41	chr1:212968400-212972000	Weak transcription	Brain Substantia Nigra	brain
42	chr1:212968400-212974400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
43	chr1:212968400-212988000	Weak transcription	Stomach Mucosa	stomach
44	chr1:212968600-212972400	Strong transcription	K562	blood
45	chr1:212968600-212980200	Weak transcription	HUVEC	blood vessel
46	chr1:212968800-212974600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr1:212969000-212971000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr1:212969000-212971200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr1:212969000-212972000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr1:212969000-212972400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood

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