Variant report

Variant	rs10240848
Chromosome Location	chr7:38406877-38406878
allele	C/T
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	IRF4	chr7:38406840-38407352	GM12878	blood:	n/a	n/a
2	SPI1	chr7:38406858-38407187	GM12891	blood:	n/a	n/a
3	TCF3	chr7:38406856-38407320	GM12878	blood:	n/a	n/a
4	PAX5	chr7:38406832-38407302	GM12878	blood:	n/a	n/a
5	TCF12	chr7:38406842-38407289	GM12878	blood:	n/a	n/a
6	POU2F2	chr7:38406841-38407222	GM12878	blood:	n/a	n/a
7	EBF1	chr7:38406862-38407380	GM12878	blood:	n/a	chr7:38407190-38407201

Variant related genes	Relation type
TRGV2	TF binding region

Extended variants
information (count: 42 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10233345	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10250122	0.99[ASN][1000 genomes]
rs10250848	0.82[ASN][1000 genomes]
rs2534590	0.83[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap]
rs28620617	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2907763	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2975065	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3735091	0.94[ASN][1000 genomes]
rs4377863	0.85[ASN][1000 genomes]
rs7793892	0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:32 , 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	nsv1027803	chr7:38257707-38410660	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
8	nsv538820	chr7:38257707-38410660	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
9	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
10	nsv820039	chr7:38289515-38411222	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
11	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
12	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
13	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
14	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
15	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
16	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
17	esv1803652	chr7:38372659-38407572	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
18	nsv966780	chr7:38374343-38407875	Enhancers Flanking Active TSS Genic enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
19	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
20	esv1850821	chr7:38378932-38411586	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	12 gene(s)	inside rSNPs	diseases
21	esv1847734	chr7:38379798-38408244	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
22	nsv5707	chr7:38380984-38407182	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
23	esv1801754	chr7:38383309-38411786	Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
24	esv1796040	chr7:38383509-38407248	Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
25	esv1801707	chr7:38383509-38411586	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
26	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
27	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
28	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
29	esv1849113	chr7:38387508-38411786	Enhancers Flanking Active TSS Genic enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
30	esv17473	chr7:38387926-38407761	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
31	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
32	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:13)

SNP	Gene	Cis/trans	Tissue	Source
rs10240848	TRGV4	cis	Esophagus Mucosa	GTEx
rs10240848	TRGV4	cis	Whole Blood	GTEx
rs10240848	TRGV4	cis	lung	GTEx
rs10240848	LOC648852	N/A	lymphoblastoid	RTeQTL
rs10240848	TRGV3	cis	Whole Blood	GTEx
rs10240848	TRGV3	cis	lung	GTEx
rs10240848	TRGV5	Cis_1M	lymphoblastoid	RTeQTL
rs10240848	TRGV5	cis	lung	GTEx
rs10240848	TRGV4	cis	Thyroid	GTEx
rs10240848	TRGV5P	cis	lung	GTEx
rs10240848	TRGV4	cis	Adipose Subcutaneous	GTEx
rs10240848	TRGV4	cis	Nerve Tibial	GTEx
rs10240848	TRGV5	cis	Whole Blood	GTEx

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:38381400-38408000	Weak transcription	Right Atrium	heart
2	chr7:38389600-38413800	Weak transcription	K562	blood
3	chr7:38398600-38414600	Weak transcription	Placenta	Placenta
4	chr7:38402800-38408000	Weak transcription	Primary neutrophils fromperipheralblood	blood
5	chr7:38403400-38407200	Weak transcription	Primary B cells from cord blood	blood
6	chr7:38403600-38407200	Weak transcription	Monocytes-CD14+_RO01746	blood
7	chr7:38404400-38410800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
8	chr7:38404800-38407400	Enhancers	Dnd41	blood
9	chr7:38405400-38407200	Enhancers	Primary T helper cells PMA-I stimulated	--
10	chr7:38406000-38407200	Enhancers	Primary T helper cells fromperipheralblood	blood
11	chr7:38406000-38407200	Enhancers	Primary T killer memory cells from peripheral blood	blood
12	chr7:38406200-38410200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr7:38406200-38410600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
14	chr7:38406200-38410800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
15	chr7:38406400-38407000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
16	chr7:38406400-38407200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr7:38406400-38407200	Enhancers	Fetal Thymus	thymus
18	chr7:38406400-38408200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr7:38406400-38408600	Enhancers	Duodenum Mucosa	Duodenum
20	chr7:38406400-38408600	Enhancers	Fetal Intestine Large	intestine
21	chr7:38406400-38409800	Enhancers	Primary hematopoietic stem cells short term culture	blood
22	chr7:38406400-38410200	Enhancers	Primary hematopoietic stem cells	blood
23	chr7:38406600-38407200	Enhancers	Primary T cells fromperipheralblood	blood
24	chr7:38406600-38407400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr7:38406600-38407400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
26	chr7:38406600-38410200	Enhancers	Primary monocytes fromperipheralblood	blood
27	chr7:38406800-38407000	Enhancers	Fetal Muscle Trunk	muscle
28	chr7:38406800-38407000	Flanking Active TSS	Thymus	Thymus
29	chr7:38406800-38407000	Enhancers	Spleen	Spleen
30	chr7:38406800-38407000	Flanking Active TSS	GM12878-XiMat	blood
31	chr7:38406800-38407400	Flanking Active TSS	Primary T cells from cord blood	blood
32	chr7:38406800-38407400	Enhancers	Muscle Satellite Cultured Cells	--
33	chr7:38406800-38407400	Enhancers	HSMMtube	muscle
34	chr7:38406800-38407600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
35	chr7:38406800-38407600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
36	chr7:38406800-38407600	Enhancers	Osteobl	bone
37	chr7:38406800-38408000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
38	chr7:38406800-38408200	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
39	chr7:38406800-38408200	Enhancers	Fetal Intestine Small	intestine
40	chr7:38406800-38408600	Enhancers	Primary B cells from peripheral blood	blood

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