Variant report

Variant	rs62445058
Chromosome Location	chr7:38412118-38412119
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr7:38411944-38412259	H1-neurons	neurons:	n/a	n/a

Variant related genes	Relation type
TRGV1	TF binding region

Extended variants
information (count: 30 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10228399	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10229383	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10262443	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1058655	0.83[ASN][1000 genomes]
rs2072505	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2160195	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55682581	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62445013	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62445016	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62446760	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73118115	0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:19 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758112	chr7:38218703-38523455	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
2	esv2759524	chr7:38218703-38523455	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
3	nsv427776	chr7:38218703-38523455	Genic enhancers Transcr. at gene 5' and 3' Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
4	nsv1025974	chr7:38227528-38503472	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
5	nsv538819	chr7:38227528-38503472	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
6	nsv932229	chr7:38248340-38727527	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
7	nsv1020990	chr7:38257707-38503472	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
8	esv2757222	chr7:38294079-38418165	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
9	nsv519863	chr7:38318590-38417556	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
10	nsv1019941	chr7:38319437-38472680	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
11	nsv1031936	chr7:38319437-38503472	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
12	nsv429745	chr7:38323485-38470561	Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
13	nsv830965	chr7:38350614-38521047	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
14	nsv1016350	chr7:38378718-38418165	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
15	nsv1020630	chr7:38384841-38415389	Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
16	nsv1021462	chr7:38384841-38418165	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
17	nsv1032769	chr7:38384841-38418465	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
18	nsv1034617	chr7:38391353-38415389	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
19	nsv830966	chr7:38393663-38602553	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs62445058	TRGV5	cis	lung	GTEx
rs62445058	TRGV4	cis	Adipose Subcutaneous	GTEx
rs62445058	TRGV4	cis	Esophagus Mucosa	GTEx
rs62445058	TRGV4	cis	lung	GTEx
rs62445058	LOC648852	N/A	lymphoblastoid	RTeQTL
rs62445058	TRGV5P	cis	lung	GTEx
rs62445058	TRGV4	cis	Whole Blood	GTEx
rs62445058	TRGV5	cis	Whole Blood	GTEx
rs62445058	TRGV5	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:38389600-38413800	Weak transcription	K562	blood
2	chr7:38398600-38414600	Weak transcription	Placenta	Placenta
3	chr7:38407000-38412800	Weak transcription	Fetal Muscle Trunk	muscle
4	chr7:38407600-38412200	Enhancers	Primary T killer memory cells from peripheral blood	blood
5	chr7:38408200-38418000	Weak transcription	Pancreas	Pancrea
6	chr7:38408400-38412800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr7:38409600-38412600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr7:38409600-38412800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr7:38409600-38412800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr7:38409600-38412800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr7:38409600-38423600	Weak transcription	Fetal Kidney	kidney
12	chr7:38409800-38421200	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr7:38409800-38438600	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr7:38410000-38412400	Weak transcription	Fetal Muscle Leg	muscle
15	chr7:38410000-38412600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr7:38410000-38412800	Weak transcription	Spleen	Spleen
17	chr7:38410000-38415200	Weak transcription	GM12878-XiMat	blood
18	chr7:38410000-38420800	Strong transcription	Dnd41	blood
19	chr7:38410000-38421800	Weak transcription	Fetal Intestine Small	intestine
20	chr7:38410000-38432800	Weak transcription	Monocytes-CD14+_RO01746	blood
21	chr7:38410200-38412200	Weak transcription	Primary monocytes fromperipheralblood	blood
22	chr7:38410200-38412800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr7:38410200-38414200	Weak transcription	Primary B cells from peripheral blood	blood
24	chr7:38410200-38419800	Weak transcription	Primary hematopoietic stem cells	blood
25	chr7:38410200-38424400	Weak transcription	Fetal Intestine Large	intestine
26	chr7:38410400-38413200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr7:38410400-38414800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
28	chr7:38410400-38419200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
29	chr7:38410600-38415200	Weak transcription	Primary T helper cells fromperipheralblood	blood
30	chr7:38410800-38422000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
31	chr7:38411200-38412200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
32	chr7:38411200-38417600	Strong transcription	Primary T cells from cord blood	blood
33	chr7:38411200-38423200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr7:38411600-38412400	Enhancers	Pancreatic Islets	Pancreatic Islet
35	chr7:38411600-38412800	Strong transcription	Primary T cells fromperipheralblood	blood
36	chr7:38411800-38412200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr7:38411800-38415000	Weak transcription	Fetal Thymus	thymus
38	chr7:38411800-38417800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
39	chr7:38412000-38413200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
40	chr7:38412000-38413200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
41	chr7:38412000-38413200	Strong transcription	Thymus	Thymus
42	chr7:38412000-38415200	Weak transcription	Primary T helper cells PMA-I stimulated	--

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