Variant report

Variant	rs62394542
Chromosome Location	chr6:25991235-25991236
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	POLR2A	chr6:25991074-25993460	GM12878	blood:	n/a	n/a
2	POLR2A	chr6:25981126-25993466	K562	blood:	n/a	n/a
3	POLR2A	chr6:25991028-25994358	MCF10A-Er-Src	breast:	n/a	n/a
4	POLR2A	chr6:25991169-25993495	GM12878	blood:	n/a	n/a
5	POLR2A	chr6:25991140-25993874	GM12891	blood:	n/a	n/a
6	POLR2A	chr6:25991162-25993610	GM18505	blood:	n/a	n/a
7	JUN	chr6:25991170-25993698	K562	blood:	n/a	chr6:25992708-25992717 chr6:25992731-25992740

No.	Distal block	Cell Line	Cell type
1	chr6:25936595..25939147-chr6:25991124..25992808,2	MCF-7	breast:
2	chr6:25962020..25964518-chr6:25991024..25993046,2	MCF-7	breast:
3	chr6:25990980..25994781-chr6:26019644..26023390,9	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TRIM38-3	chr6:25990989-25991454	ENSG00000272065.1

Variant related genes	Relation type
ENSG00000272462	TF binding region
ENSG00000112343	Chromatin interaction
ENSG00000198366	Chromatin interaction
ENSG00000196176	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10484434	0.95[EUR][1000 genomes]
rs11751732	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11755492	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11756400	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11758378	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11759668	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11961143	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11965426	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2051538	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2230654	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34956419	0.86[ASN][1000 genomes]
rs36125084	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3799374	0.86[ASN][1000 genomes]
rs41266783	0.95[EUR][1000 genomes]
rs55661658	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56073264	0.86[ASN][1000 genomes]
rs59281021	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61289224	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62000984	0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62394540	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62394550	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62394555	0.86[ASN][1000 genomes]
rs62394556	0.86[ASN][1000 genomes]
rs62396160	0.86[ASN][1000 genomes]
rs62396164	0.86[ASN][1000 genomes]
rs66505449	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs66536062	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6906460	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6925912	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6935470	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7746105	0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs7757646	0.86[ASN][1000 genomes]
rs7773526	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9689245	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 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	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
8	nsv1015627	chr6:25973495-26100483	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	447 gene(s)	inside rSNPs	diseases
9	nsv538164	chr6:25973495-26100483	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	447 gene(s)	inside rSNPs	diseases
10	nsv1028456	chr6:25984457-26174993	Active TSS Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	873 gene(s)	inside rSNPs	diseases
11	nsv538165	chr6:25984457-26174993	Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	873 gene(s)	inside rSNPs	diseases
12	nsv428137	chr6:25987413-26351920	Enhancers Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1181 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs62394542	TRIM38	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25967200-25992000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr6:25967800-25992000	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr6:25972800-25992000	Weak transcription	Right Ventricle	heart
4	chr6:25974800-25992000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr6:25974800-25992000	Weak transcription	A549	lung
6	chr6:25976400-25992000	Weak transcription	NH-A	brain
7	chr6:25982800-25992000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr6:25983000-25992000	Weak transcription	Brain Substantia Nigra	brain
9	chr6:25983800-25992000	Weak transcription	Pancreas	Pancrea
10	chr6:25983800-25992000	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr6:25983800-25992200	Weak transcription	Gastric	stomach
12	chr6:25984000-25992000	Weak transcription	Small Intestine	intestine
13	chr6:25984000-25992200	Weak transcription	Stomach Mucosa	stomach
14	chr6:25984200-25992000	Weak transcription	NHEK	skin
15	chr6:25984400-25991400	Weak transcription	Hela-S3	cervix
16	chr6:25984400-25991600	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr6:25984400-25991600	Weak transcription	Dnd41	blood
18	chr6:25984400-25992000	Weak transcription	Colonic Mucosa	Colon
19	chr6:25984400-25992000	Weak transcription	Ovary	ovary
20	chr6:25984400-25992000	Weak transcription	Psoas Muscle	Psoas
21	chr6:25984600-25991400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
22	chr6:25984600-25992000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr6:25984800-25992000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr6:25984800-25992000	Weak transcription	Colon Smooth Muscle	Colon
25	chr6:25984800-25992000	Weak transcription	Esophagus	oesophagus
26	chr6:25984800-25992000	Weak transcription	Fetal Kidney	kidney
27	chr6:25985000-25992000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr6:25985200-25992000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
29	chr6:25985400-25991600	Weak transcription	Primary T helper cells PMA-I stimulated	--
30	chr6:25985400-25992000	Weak transcription	Left Ventricle	heart
31	chr6:25985800-25991600	Weak transcription	HUVEC	blood vessel
32	chr6:25985800-25992000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
33	chr6:25985800-25992000	Weak transcription	Fetal Lung	lung
34	chr6:25986000-25992000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
35	chr6:25986000-25992000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
36	chr6:25986000-25992000	Weak transcription	HMEC	breast
37	chr6:25986200-25991400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
38	chr6:25986200-25991600	Weak transcription	NHDF-Ad	bronchial
39	chr6:25986400-25991600	Weak transcription	Liver	Liver
40	chr6:25986600-25991800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr6:25986800-25991800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr6:25987000-25992000	Weak transcription	Fetal Thymus	thymus
43	chr6:25987200-25991600	Weak transcription	Duodenum Mucosa	Duodenum
44	chr6:25987200-25992000	Weak transcription	Skeletal Muscle Female	skeletal muscle
45	chr6:25987400-25991600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr6:25987800-25992000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr6:25988000-25992000	Weak transcription	Placenta	Placenta
48	chr6:25988200-25991600	Weak transcription	HUES48 Cell Line	embryonic stem cell
49	chr6:25988200-25991600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
50	chr6:25988200-25992200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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