Variant report

Variant	rs7513734
Chromosome Location	chr1:212940510-212940511
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 64 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10127613	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1032963	0.86[EUR][1000 genomes]
rs1032964	0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10779583	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10863992	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10864002	0.89[EUR][1000 genomes]
rs11120005	0.95[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs11120034	0.89[EUR][1000 genomes]
rs11120038	0.85[EUR][1000 genomes]
rs12133194	0.86[EUR][1000 genomes]
rs12239017	0.88[EUR][1000 genomes]
rs12568552	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12744555	0.89[EUR][1000 genomes]
rs12757944	0.89[EUR][1000 genomes]
rs1507359	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs15702	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1580991	0.82[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs1580992	0.82[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs1605420	0.87[EUR][1000 genomes]
rs1813705	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1848243	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2292214	0.95[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2884675	0.89[EUR][1000 genomes]
rs3738802	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3949369	0.89[EUR][1000 genomes]
rs4520475	0.84[ASN][1000 genomes]
rs4639827	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4951464	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4951639	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6540766	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6540767	0.89[EUR][1000 genomes]
rs6665489	0.81[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs6670373	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6670869	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6678961	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6681851	0.86[EUR][1000 genomes]
rs6685864	0.86[EUR][1000 genomes]
rs6686145	0.85[EUR][1000 genomes]
rs6686164	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6689799	0.85[EUR][1000 genomes]
rs6694887	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6696870	0.86[EUR][1000 genomes]
rs6696908	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6700465	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6702544	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6703982	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7513199	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7513210	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7513772	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7514070	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7522100	0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7528303	0.89[EUR][1000 genomes]
rs7535608	0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7538853	0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7543603	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7547100	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7555930	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][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	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
5	nsv1005983	chr1:212917531-212947521	ZNF genes & repeats Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	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
7	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

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs7513734	FLVCR1-AS1	cis	Adipose Subcutaneous	GTEx
rs7513734	FLVCR1	Cis_1M	lymphoblastoid	RTeQTL
rs7513734	NSL1	Cis_1M	lymphoblastoid	RTeQTL
rs7513734	FLVCR1-AS1	cis	Esophagus Muscularis	GTEx
rs7513734	FLVCR1-AS1	cis	Whole Blood	GTEx
rs7513734	LQK1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212895400-212964600	Weak transcription	Pancreas	Pancrea
2	chr1:212895600-212964600	Weak transcription	Gastric	stomach
3	chr1:212901400-212954000	Weak transcription	NH-A	brain
4	chr1:212902200-212941800	Weak transcription	Fetal Kidney	kidney
5	chr1:212902600-212943600	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr1:212915400-212942000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr1:212923600-212956200	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr1:212923600-212963800	Weak transcription	Brain Angular Gyrus	brain
9	chr1:212923600-212964400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr1:212923800-212947200	Weak transcription	A549	lung
11	chr1:212923800-212957600	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr1:212923800-212964200	Weak transcription	HMEC	breast
13	chr1:212924000-212954200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr1:212926600-212941800	Weak transcription	Stomach Smooth Muscle	stomach
15	chr1:212926600-212954200	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr1:212926600-212963400	Weak transcription	Rectal Smooth Muscle	rectum
17	chr1:212926800-212940600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr1:212926800-212940800	Weak transcription	NHLF	lung
19	chr1:212926800-212942200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr1:212926800-212942400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr1:212926800-212942800	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr1:212926800-212942800	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr1:212926800-212947800	Weak transcription	NHDF-Ad	bronchial
24	chr1:212926800-212948000	Weak transcription	Osteobl	bone
25	chr1:212926800-212954200	Weak transcription	Hela-S3	cervix
26	chr1:212927000-212941800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr1:212927400-212942400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr1:212927400-212963400	Weak transcription	Small Intestine	intestine
29	chr1:212927400-212964200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr1:212928200-212942400	Weak transcription	HUES64 Cell Line	embryonic stem cell
31	chr1:212928400-212941800	Weak transcription	Brain Anterior Caudate	brain
32	chr1:212928400-212941800	Weak transcription	Brain Cingulate Gyrus	brain
33	chr1:212928400-212942000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr1:212928400-212942000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
35	chr1:212928400-212942200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr1:212928400-212942200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr1:212928400-212954000	Weak transcription	Fetal Brain Male	brain
38	chr1:212928400-212956200	Weak transcription	Sigmoid Colon	Sigmoid Colon
39	chr1:212928600-212940600	Weak transcription	Primary T helper cells PMA-I stimulated	--
40	chr1:212928600-212942200	Weak transcription	Brain Hippocampus Middle	brain
41	chr1:212928600-212942400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
42	chr1:212928600-212942400	Weak transcription	Brain Substantia Nigra	brain
43	chr1:212928600-212947800	Weak transcription	HUES48 Cell Line	embryonic stem cell
44	chr1:212928600-212954200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
45	chr1:212929000-212947800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr1:212930600-212941800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
47	chr1:212933800-212942000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
48	chr1:212933800-212943000	Weak transcription	Colonic Mucosa	Colon
49	chr1:212934200-212952400	Weak transcription	H1 Cell Line	embryonic stem cell
50	chr1:212935000-212942000	Weak transcription	HepG2	liver

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