Variant report

Variant	rs6700465
Chromosome Location	chr1:212908929-212908930
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:212900728..212905676-chr1:212905955..212909387,7	K562	blood:
2	chr1:212903641..212909081-chr1:212909543..212915352,7	K562	blood:
3	chr1:212908280..212910859-chr1:212913083..212914698,2	K562	blood:

Extended variants
information (count: 59 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10127613	0.90[AFR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1032963	0.86[EUR][1000 genomes]
rs1032964	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10779583	0.92[EUR][1000 genomes]
rs10863992	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10864002	0.91[EUR][1000 genomes]
rs11120005	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11120034	0.91[EUR][1000 genomes]
rs11120038	0.87[EUR][1000 genomes]
rs12133194	0.87[EUR][1000 genomes]
rs12239017	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12568552	0.86[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs12744555	0.91[EUR][1000 genomes]
rs12757944	0.91[EUR][1000 genomes]
rs1507359	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs15702	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1580991	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1580992	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1605420	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1813705	0.93[EUR][1000 genomes]
rs1848243	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2292214	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2884675	0.91[EUR][1000 genomes]
rs3738802	0.93[AFR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3949369	0.91[EUR][1000 genomes]
rs4639827	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4951639	0.89[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs6540766	0.93[EUR][1000 genomes]
rs6540767	0.91[EUR][1000 genomes]
rs6665489	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6670373	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6670869	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6678961	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6681851	0.87[EUR][1000 genomes]
rs6685864	0.87[EUR][1000 genomes]
rs6686145	0.87[EUR][1000 genomes]
rs6686164	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6689799	0.86[EUR][1000 genomes]
rs6694887	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6696870	0.87[EUR][1000 genomes]
rs6696908	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6702544	0.89[AFR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6703982	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7513199	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7513210	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7513734	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7513772	0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7514070	0.98[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7522100	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7528303	0.91[EUR][1000 genomes]
rs7535608	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7538853	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7543603	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7547100	0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7555930	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[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	nsv1013110	chr1:212555764-212948092	Flanking Active TSS Bivalent/Poised TSS Strong transcription Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	81 gene(s)	inside rSNPs	diseases
2	nsv535287	chr1:212555764-212948092	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	81 gene(s)	inside rSNPs	diseases
3	nsv549148	chr1:212876902-212962207	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
4	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

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs6700465	LQK1	Cis_1M	lymphoblastoid	RTeQTL
rs6700465	FLVCR1-AS1	cis	Esophagus Muscularis	GTEx
rs6700465	NSL1	Cis_1M	lymphoblastoid	RTeQTL
rs6700465	FLVCR1	Cis_1M	lymphoblastoid	RTeQTL
rs6700465	FLVCR1-AS1	cis	Adipose Subcutaneous	GTEx
rs6700465	FLVCR1-AS1	cis	Whole Blood	GTEx

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212895200-212922800	Weak transcription	Left Ventricle	heart
2	chr1:212895400-212912000	Weak transcription	Primary T cells fromperipheralblood	blood
3	chr1:212895400-212914600	Weak transcription	Spleen	Spleen
4	chr1:212895400-212916600	Weak transcription	Primary T helper cells fromperipheralblood	blood
5	chr1:212895400-212917400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr1:212895400-212923200	Weak transcription	Brain Cingulate Gyrus	brain
7	chr1:212895400-212923400	Weak transcription	Fetal Muscle Leg	muscle
8	chr1:212895400-212923400	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr1:212895400-212926400	Weak transcription	Esophagus	oesophagus
10	chr1:212895400-212964600	Weak transcription	Pancreas	Pancrea
11	chr1:212895600-212923000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr1:212895600-212923400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr1:212895600-212964600	Weak transcription	Gastric	stomach
14	chr1:212895800-212911200	Weak transcription	Primary T helper cells PMA-I stimulated	--
15	chr1:212895800-212917400	Weak transcription	NHLF	lung
16	chr1:212895800-212925600	Weak transcription	Small Intestine	intestine
17	chr1:212895800-212926200	Weak transcription	Hela-S3	cervix
18	chr1:212896000-212911800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
19	chr1:212896000-212917000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr1:212896200-212912200	Weak transcription	Primary hematopoietic stem cells	blood
21	chr1:212896400-212917000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr1:212896800-212909000	Weak transcription	Primary B cells from cord blood	blood
23	chr1:212897400-212914600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr1:212897800-212911600	Weak transcription	Brain Germinal Matrix	brain
25	chr1:212898400-212909600	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr1:212898600-212923200	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr1:212898800-212911800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr1:212898800-212934000	Weak transcription	Fetal Muscle Trunk	muscle
29	chr1:212899200-212914600	Weak transcription	Ovary	ovary
30	chr1:212899800-212926400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr1:212900000-212910800	Weak transcription	Brain Substantia Nigra	brain
32	chr1:212900000-212911000	Weak transcription	HUES64 Cell Line	embryonic stem cell
33	chr1:212900400-212914600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr1:212900400-212914600	Weak transcription	HUES6 Cell Line	embryonic stem cell
35	chr1:212900400-212917400	Weak transcription	Fetal Stomach	stomach
36	chr1:212900400-212923200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr1:212900400-212927600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr1:212900400-212932600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr1:212900400-212936200	Weak transcription	Aorta	Aorta
40	chr1:212900600-212911800	Weak transcription	Psoas Muscle	Psoas
41	chr1:212901000-212911400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr1:212901400-212954000	Weak transcription	NH-A	brain
43	chr1:212901600-212911800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr1:212901600-212914400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr1:212901600-212923000	Weak transcription	HSMM	muscle
46	chr1:212901800-212911400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr1:212902000-212909600	Weak transcription	Primary neutrophils fromperipheralblood	blood
48	chr1:212902200-212911800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
49	chr1:212902200-212912600	Weak transcription	Brain Angular Gyrus	brain
50	chr1:212902200-212941800	Weak transcription	Fetal Kidney	kidney

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