Variant report

Variant	rs6871999
Chromosome Location	chr5:40694797-40694798
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 54 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10056345	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10060234	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10064175	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1097546	0.85[ASN][1000 genomes]
rs13354346	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13355305	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs154268	0.85[ASN][1000 genomes]
rs154275	0.85[ASN][1000 genomes]
rs154280	0.85[ASN][1000 genomes]
rs154284	0.85[ASN][1000 genomes]
rs1644962	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs171605	0.85[ASN][1000 genomes]
rs193864	0.83[ASN][1000 genomes]
rs2161521	0.85[ASN][1000 genomes]
rs249413	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs249414	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs249416	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs249420	0.83[ASN][1000 genomes]
rs249422	0.85[ASN][1000 genomes]
rs249423	0.85[ASN][1000 genomes]
rs249425	0.85[ASN][1000 genomes]
rs249428	0.85[ASN][1000 genomes]
rs249429	0.85[ASN][1000 genomes]
rs257009	0.84[ASN][1000 genomes]
rs28569300	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs29740	0.85[ASN][1000 genomes]
rs29742	0.85[ASN][1000 genomes]
rs29743	0.85[ASN][1000 genomes]
rs29744	0.85[ASN][1000 genomes]
rs4277957	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4285273	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4315964	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4315965	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs432071	0.85[ASN][1000 genomes]
rs434778	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4383756	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs447810	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs453037	0.85[ASN][1000 genomes]
rs4546432	0.83[AFR][1000 genomes]
rs4573034	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs461404	0.85[ASN][1000 genomes]
rs466108	0.85[ASN][1000 genomes]
rs466962	0.83[ASN][1000 genomes]
rs4957344	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59069340	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59920139	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6451535	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6451537	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6896993	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7708680	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7726237	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7737044	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs837101	0.84[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv880539	chr5:40662257-40713645	Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6871999	RPL37	Cis_1M	lymphoblastoid	RTeQTL
rs6871999	TTC33	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:40684000-40700600	Weak transcription	Left Ventricle	heart
2	chr5:40684600-40700400	Weak transcription	Right Ventricle	heart
3	chr5:40688400-40696400	Weak transcription	Liver	Liver
4	chr5:40688400-40700400	Weak transcription	Stomach Mucosa	stomach
5	chr5:40688800-40696800	Weak transcription	Fetal Lung	lung
6	chr5:40688800-40697000	Strong transcription	Fetal Thymus	thymus
7	chr5:40688800-40718600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr5:40690000-40695800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr5:40690200-40695200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
10	chr5:40690400-40695200	Strong transcription	HSMM	muscle
11	chr5:40690400-40697200	Strong transcription	Monocytes-CD14+_RO01746	blood
12	chr5:40690600-40695400	Strong transcription	Duodenum Mucosa	Duodenum
13	chr5:40690800-40694800	Strong transcription	HUVEC	blood vessel
14	chr5:40690800-40695800	Weak transcription	A549	lung
15	chr5:40691200-40694800	Strong transcription	Primary neutrophils fromperipheralblood	blood
16	chr5:40691200-40695200	Strong transcription	Primary monocytes fromperipheralblood	blood
17	chr5:40691200-40697000	Strong transcription	Primary T cells from cord blood	blood
18	chr5:40691400-40695000	Strong transcription	Primary B cells from peripheral blood	blood
19	chr5:40691600-40695200	Strong transcription	Adipose Nuclei	Adipose
20	chr5:40691600-40695400	Strong transcription	Muscle Satellite Cultured Cells	--
21	chr5:40692200-40701800	Weak transcription	Colon Smooth Muscle	Colon
22	chr5:40692400-40695200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr5:40692400-40741200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
24	chr5:40692600-40698600	Weak transcription	HSMMtube	muscle
25	chr5:40692800-40694800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
26	chr5:40692800-40695200	Strong transcription	Dnd41	blood
27	chr5:40692800-40700400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr5:40692800-40700400	Weak transcription	Esophagus	oesophagus
29	chr5:40692800-40700400	Weak transcription	Gastric	stomach
30	chr5:40692800-40700400	Weak transcription	Pancreas	Pancrea
31	chr5:40692800-40700400	Weak transcription	Small Intestine	intestine
32	chr5:40692800-40700600	Strong transcription	Primary T cells fromperipheralblood	blood
33	chr5:40692800-40702400	Weak transcription	Colonic Mucosa	Colon
34	chr5:40692800-40721000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr5:40692800-40733800	Weak transcription	Skeletal Muscle Male	skeletal muscle
36	chr5:40692800-40735000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr5:40693000-40694800	Genic enhancers	Primary T helper cells PMA-I stimulated	--
38	chr5:40693000-40694800	Weak transcription	NHEK	skin
39	chr5:40693000-40698200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
40	chr5:40693000-40700800	Weak transcription	Fetal Muscle Trunk	muscle
41	chr5:40693000-40701800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
42	chr5:40693000-40701800	Weak transcription	Duodenum Smooth Muscle	Duodenum
43	chr5:40693000-40702000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr5:40693000-40702000	Weak transcription	Rectal Smooth Muscle	rectum
45	chr5:40693600-40696600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr5:40693600-40727400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr5:40693800-40695400	Weak transcription	NH-A	brain
48	chr5:40693800-40700000	Strong transcription	Primary T helper cells fromperipheralblood	blood
49	chr5:40694200-40694800	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr5:40694200-40694800	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung

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