Variant report

Variant	rs6540766
Chromosome Location	chr1:212970215-212970216
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:212873187..212876182-chr1:212968130..212971085,2	K562	blood:

Variant related genes	Relation type
ENSG00000123685	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10127613	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1021994	0.87[ASN][1000 genomes]
rs1032962	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1032963	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1032964	0.93[EUR][1000 genomes]
rs1032965	0.91[ASN][1000 genomes]
rs10779583	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10863992	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10864002	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11120005	0.86[EUR][1000 genomes]
rs11120028	0.96[ASN][1000 genomes]
rs11120034	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11120038	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12038225	0.88[ASN][1000 genomes]
rs12124669	0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12133194	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12239017	0.83[EUR][1000 genomes]
rs12568552	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12744555	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12757944	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1507359	0.93[EUR][1000 genomes]
rs15702	0.93[EUR][1000 genomes]
rs1580991	0.85[EUR][1000 genomes]
rs1580992	0.85[EUR][1000 genomes]
rs1605420	0.82[EUR][1000 genomes]
rs1813705	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1848243	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2292214	0.91[EUR][1000 genomes]
rs2456818	0.92[ASN][1000 genomes]
rs2456827	0.96[ASN][1000 genomes]
rs2456828	0.88[ASN][1000 genomes]
rs2884675	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3738800	0.96[ASN][1000 genomes]
rs3738802	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3949369	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4639827	0.93[EUR][1000 genomes]
rs4951464	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4951639	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6540767	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6665489	0.85[EUR][1000 genomes]
rs6670373	0.85[EUR][1000 genomes]
rs6670869	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6678961	0.85[EUR][1000 genomes]
rs6681851	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6685864	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6686145	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6686164	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6689799	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6694887	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6696870	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6696908	0.82[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs6700465	0.93[EUR][1000 genomes]
rs6702544	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6703982	0.85[EUR][1000 genomes]
rs7513199	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7513210	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7513734	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7513772	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7514070	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7522100	0.93[EUR][1000 genomes]
rs7528303	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7535608	0.93[EUR][1000 genomes]
rs7538853	0.93[EUR][1000 genomes]
rs7543603	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7547100	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7555930	0.89[AMR][1000 genomes];0.90[EUR][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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs6540766	NSL1	Cis_1M	lymphoblastoid	RTeQTL
rs6540766	LQK1	Cis_1M	lymphoblastoid	RTeQTL
rs6540766	FLVCR1	Cis_1M	lymphoblastoid	RTeQTL
rs6540766	FLVCR1-AS1	cis	Esophagus Muscularis	GTEx
rs6540766	FLVCR1-AS1	cis	Adipose Subcutaneous	GTEx
rs6540766	FLVCR1-AS1	cis	lung	GTEx
rs6540766	FLVCR1-AS1	cis	Whole Blood	GTEx

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	chr1:212966400-212970400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr1:212966400-212970400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr1:212966400-212970400	Weak transcription	NH-A	brain
18	chr1:212966400-212972000	Weak transcription	Fetal Brain Female	brain
19	chr1:212966400-212972000	Weak transcription	Fetal Muscle Leg	muscle
20	chr1:212966400-212972000	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr1:212966400-212972000	Weak transcription	Thymus	Thymus
22	chr1:212966400-212977400	Weak transcription	Hela-S3	cervix
23	chr1:212966400-212984000	Weak transcription	Rectal Smooth Muscle	rectum
24	chr1:212966400-212985600	Weak transcription	Pancreatic Islets	Pancreatic Islet
25	chr1:212966400-212988200	Weak transcription	Fetal Heart	heart
26	chr1:212966400-212989600	Weak transcription	Fetal Brain Male	brain
27	chr1:212966400-212990200	Weak transcription	Right Ventricle	heart
28	chr1:212966600-212970400	Weak transcription	Stomach Smooth Muscle	stomach
29	chr1:212966600-212970600	Weak transcription	Rectal Mucosa Donor 31	rectum
30	chr1:212966800-212977600	Weak transcription	Brain Germinal Matrix	brain
31	chr1:212966800-212989600	Weak transcription	Psoas Muscle	Psoas
32	chr1:212967000-212970400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
33	chr1:212967000-212970800	Weak transcription	Muscle Satellite Cultured Cells	--
34	chr1:212967000-212972000	Weak transcription	NHEK	skin
35	chr1:212967000-212979000	Weak transcription	Cortex derived primary cultured neurospheres	brain
36	chr1:212967000-212984400	Weak transcription	Spleen	Spleen
37	chr1:212967200-212970600	Weak transcription	A549	lung
38	chr1:212967200-212975400	Weak transcription	HSMM	muscle
39	chr1:212967200-212984000	Weak transcription	NHDF-Ad	bronchial
40	chr1:212967200-212988400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr1:212967200-212989000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr1:212967200-212989600	Weak transcription	NHLF	lung
43	chr1:212968000-212980000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr1:212968000-212987400	Weak transcription	Fetal Intestine Large	intestine
45	chr1:212968200-212971600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr1:212968200-212972000	Weak transcription	Fetal Intestine Small	intestine
47	chr1:212968400-212970400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
48	chr1:212968400-212970400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
49	chr1:212968400-212970400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
50	chr1:212968400-212970600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood

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