Variant report

Variant	rs62443339
Chromosome Location	chr7:38258486-38258487
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:38253002..38255460-chr7:38256658..38259135,2	K562	blood:

Extended variants
information (count: 33 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs12154478	0.82[AMR][1000 genomes]
rs12155083	0.94[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs56030139	0.94[ASN][1000 genomes]
rs56045043	0.94[ASN][1000 genomes]
rs56189345	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs56356594	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62443297	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62443319	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62443320	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62443321	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62443325	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62443329	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62443335	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62443336	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62443337	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62443340	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6959603	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1016355	chr7:38168232-38372719	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
2	nsv830963	chr7:38172988-38344779	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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
6	nsv830964	chr7:38218708-38390518	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
7	nsv1030349	chr7:38227528-38372719	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
8	nsv538818	chr7:38227528-38372719	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
9	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
10	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
11	nsv433041	chr7:38229107-38358728	Strong transcription Genic enhancers Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
12	nsv433044	chr7:38238119-38358728	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
13	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
14	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
15	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
16	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs62443339	TRGC2	cis	Esophagus Mucosa	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:38218600-38259200	Weak transcription	Colonic Mucosa	Colon
2	chr7:38230200-38259200	Weak transcription	K562	blood
3	chr7:38236800-38261600	Weak transcription	HMEC	breast
4	chr7:38237600-38258600	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr7:38237800-38261600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr7:38238000-38259200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr7:38238600-38268800	Weak transcription	Esophagus	oesophagus
8	chr7:38249200-38259200	Weak transcription	Spleen	Spleen
9	chr7:38251200-38261400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr7:38251600-38270400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr7:38251800-38270200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr7:38252000-38272400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr7:38252000-38273000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr7:38253800-38267400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr7:38254200-38261600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr7:38254400-38263200	Strong transcription	HSMMtube	muscle
17	chr7:38254600-38259800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr7:38255000-38268800	Weak transcription	Gastric	stomach
19	chr7:38255400-38260200	Strong transcription	Sigmoid Colon	Sigmoid Colon
20	chr7:38255400-38264800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
21	chr7:38255400-38267400	Weak transcription	Stomach Mucosa	stomach
22	chr7:38255400-38271800	Weak transcription	Small Intestine	intestine
23	chr7:38255600-38260400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
24	chr7:38255600-38263000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
25	chr7:38255600-38264600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr7:38255600-38268600	Weak transcription	Pancreas	Pancrea
27	chr7:38255800-38259000	Weak transcription	Fetal Heart	heart
28	chr7:38255800-38261600	Strong transcription	Fetal Brain Female	brain
29	chr7:38255800-38262000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr7:38255800-38264400	Strong transcription	GM12878-XiMat	blood
31	chr7:38256000-38259200	Weak transcription	Brain Hippocampus Middle	brain
32	chr7:38256000-38260600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr7:38256000-38261800	Strong transcription	Muscle Satellite Cultured Cells	--
34	chr7:38256000-38262000	Strong transcription	Primary B cells from peripheral blood	blood
35	chr7:38256000-38263400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr7:38256000-38264400	Strong transcription	Fetal Muscle Trunk	muscle
37	chr7:38256200-38259800	Strong transcription	Aorta	Aorta
38	chr7:38256200-38260600	Strong transcription	Brain Germinal Matrix	brain
39	chr7:38256200-38261600	Strong transcription	NHLF	lung
40	chr7:38256200-38261800	Strong transcription	Duodenum Mucosa	Duodenum
41	chr7:38256200-38261800	Strong transcription	Stomach Smooth Muscle	stomach
42	chr7:38256200-38262000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr7:38256200-38262000	Strong transcription	Monocytes-CD14+_RO01746	blood
44	chr7:38256200-38262600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr7:38256200-38264400	Strong transcription	HUES48 Cell Line	embryonic stem cell
46	chr7:38256200-38264400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr7:38256200-38265400	Strong transcription	HUES64 Cell Line	embryonic stem cell
48	chr7:38256200-38268800	Strong transcription	HSMM	muscle
49	chr7:38256400-38259000	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
50	chr7:38256400-38259200	Weak transcription	Brain Substantia Nigra	brain

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