Variant report

Variant	rs62394540
Chromosome Location	chr6:25971174-25971175
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:25971021..25973495-chr6:25981225..25983155,2	K562	blood:
2	chr6:25971054..25973190-chr6:25974821..25978453,3	MCF-7	breast:
3	chr6:25968181..25971395-chr6:25974382..25976883,4	K562	blood:
4	chr6:25971001..25973533-chr6:25984145..25985680,2	MCF-7	breast:
5	chr6:25970103..25974730-chr6:25988970..25993651,6	MCF-7	breast:
6	chr6:25962466..25966949-chr6:25968245..25972653,5	MCF-7	breast:
7	chr6:25970867..25974848-chr6:25991137..25994238,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000272065	Chromatin interaction
ENSG00000112343	Chromatin interaction
ENSG00000272462	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10484434	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11751732	0.84[EUR][1000 genomes]
rs11755492	0.90[EUR][1000 genomes]
rs11756400	0.85[EUR][1000 genomes]
rs11756659	0.86[ASN][1000 genomes]
rs11758372	0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs11758378	0.87[EUR][1000 genomes]
rs11759668	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11961143	0.90[EUR][1000 genomes]
rs11965426	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2051538	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2230654	0.84[EUR][1000 genomes]
rs36125084	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs41266783	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs55661658	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs59281021	1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61289224	0.84[EUR][1000 genomes]
rs62000984	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62394537	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs62394542	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62394550	0.84[EUR][1000 genomes]
rs66505449	0.90[EUR][1000 genomes]
rs66536062	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6906460	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6925912	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6935470	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7773526	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1029920	chr6:25638507-26585842	Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1215 gene(s)	inside rSNPs	diseases
2	nsv538162	chr6:25638507-26585842	Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1215 gene(s)	inside rSNPs	diseases
3	nsv1030351	chr6:25813178-26352046	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1189 gene(s)	inside rSNPs	diseases
4	nsv1023453	chr6:25853830-26528250	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1201 gene(s)	inside rSNPs	diseases
5	nsv1025237	chr6:25874326-26280867	Flanking Active TSS Active TSS Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1166 gene(s)	inside rSNPs	diseases
6	nsv538163	chr6:25874326-26280867	Enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1166 gene(s)	inside rSNPs	diseases
7	esv2755446	chr6:25924513-25981648	Weak transcription Genic enhancers Active TSS Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
8	nsv432857	chr6:25957109-26072445	Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	451 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs62394540	TRIM38	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25964400-25974600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr6:25964400-25981400	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr6:25964600-25971400	Genic enhancers	Primary T helper cells fromperipheralblood	blood
4	chr6:25964800-25978800	Strong transcription	Fetal Thymus	thymus
5	chr6:25965000-25979200	Strong transcription	Fetal Muscle Trunk	muscle
6	chr6:25965600-25985600	Weak transcription	Brain Hippocampus Middle	brain
7	chr6:25966200-25973000	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
8	chr6:25966400-25974800	Strong transcription	HepG2	liver
9	chr6:25967000-25971800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr6:25967000-25975800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr6:25967200-25972000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr6:25967200-25972000	Weak transcription	Left Ventricle	heart
13	chr6:25967200-25972000	Weak transcription	Right Ventricle	heart
14	chr6:25967200-25972200	Weak transcription	Pancreas	Pancrea
15	chr6:25967200-25974200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr6:25967200-25977600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr6:25967200-25979200	Strong transcription	Thymus	Thymus
18	chr6:25967200-25981000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr6:25967200-25992000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr6:25967400-25971200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr6:25967600-25971800	Weak transcription	HUES64 Cell Line	embryonic stem cell
22	chr6:25967600-25972800	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr6:25967600-25973000	Genic enhancers	Primary B cells from peripheral blood	blood
24	chr6:25967800-25971200	Weak transcription	Stomach Mucosa	stomach
25	chr6:25967800-25992000	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr6:25968000-25972600	Genic enhancers	Osteobl	bone
27	chr6:25968200-25972200	Weak transcription	Colonic Mucosa	Colon
28	chr6:25968200-25972200	Strong transcription	Placenta	Placenta
29	chr6:25968400-25971200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr6:25968400-25971200	Strong transcription	Fetal Intestine Large	intestine
31	chr6:25968400-25972000	Weak transcription	Right Atrium	heart
32	chr6:25968400-25972200	Weak transcription	Fetal Stomach	stomach
33	chr6:25968400-25979600	Strong transcription	Stomach Smooth Muscle	stomach
34	chr6:25968400-25981200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr6:25968400-25985600	Strong transcription	Primary hematopoietic stem cells	blood
36	chr6:25968400-25987600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
37	chr6:25968600-25971800	Weak transcription	Aorta	Aorta
38	chr6:25968600-25972000	Weak transcription	Esophagus	oesophagus
39	chr6:25968600-25972000	Weak transcription	Spleen	Spleen
40	chr6:25968600-25972200	Weak transcription	Gastric	stomach
41	chr6:25968600-25977600	Strong transcription	Ovary	ovary
42	chr6:25968600-25978800	Strong transcription	Primary T cells fromperipheralblood	blood
43	chr6:25968600-25979200	Strong transcription	Fetal Muscle Leg	muscle
44	chr6:25968600-25986000	Strong transcription	Rectal Mucosa Donor 29	rectum
45	chr6:25968600-25987200	Strong transcription	Duodenum Mucosa	Duodenum
46	chr6:25968800-25971200	Genic enhancers	Muscle Satellite Cultured Cells	--
47	chr6:25968800-25971200	Strong transcription	Duodenum Smooth Muscle	Duodenum
48	chr6:25968800-25971400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr6:25968800-25979200	Strong transcription	Sigmoid Colon	Sigmoid Colon
50	chr6:25968800-25986600	Strong transcription	Rectal Mucosa Donor 31	rectum

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