Variant report

Variant	rs62000984
Chromosome Location	chr6:26017675-26017676
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:27)
CpG islands
(count:0)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:27 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAFK	chr6:26017649-26018181	IMR90	lung:	n/a	n/a
2	POLR2A	chr6:26017499-26018182	U87	brain:	n/a	n/a
3	TAF1	chr6:26017628-26018315	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr6:26017499-26018146	U87	brain:	n/a	n/a
5	POLR2A	chr6:26017417-26018598	H1-hESC	embryonic stem cell:	n/a	n/a
6	POLR2A	chr6:26017668-26018107	GM12878	blood:	n/a	n/a
7	POLR2A	chr6:26017244-26018326	U87	brain:	n/a	n/a
8	POLR2A	chr6:26016918-26018312	HUVEC	blood vessel:	n/a	n/a
9	POLR2A	chr6:26017582-26018302	HUVEC	blood vessel:	n/a	n/a
10	POLR2A	chr6:26017442-26018208	U87	brain:	n/a	n/a
11	POLR2A	chr6:26017649-26018244	GM12892	blood:	n/a	n/a
12	POLR2A	chr6:26017225-26018210	H1-hESC	embryonic stem cell:	n/a	n/a
13	POLR2A	chr6:26017451-26018314	HUVEC	blood vessel:	n/a	n/a
14	MYC	chr6:26017047-26018076	MCF10A-Er-Src	breast:	n/a	n/a
15	POLR2A	chr6:26017671-26018153	GM12892	blood:	n/a	n/a
16	ELF1	chr6:26017492-26018269	GM12878	blood:	n/a	n/a
17	POLR2A	chr6:26016551-26018222	H1-hESC	embryonic stem cell:	n/a	n/a
18	POLR2A	chr6:26017415-26018207	HUVEC	blood vessel:	n/a	n/a
19	ATF2	chr6:26017065-26017919	H1-hESC	embryonic stem cell:	n/a	n/a
20	RCOR1	chr6:26016562-26018786	IMR90	lung:	n/a	n/a
21	MAZ	chr6:26017202-26018460	IMR90	lung:	n/a	n/a
22	POLR2A	chr6:26016538-26018308	H1-hESC	embryonic stem cell:	n/a	n/a
23	POLR2A	chr6:26017537-26018159	GM12878	blood:	n/a	n/a
24	POLR2A	chr6:26017598-26018201	GM12892	blood:	n/a	n/a
25	TAF7	chr6:26016766-26018365	H1-hESC	embryonic stem cell:	n/a	n/a
26	POLR2A	chr6:26017540-26018164	H1-hESC	embryonic stem cell:	n/a	n/a
27	POLR2A	chr6:26017583-26018279	IMR90	lung:	n/a	n/a

No data

(count:1 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:26016695..26019436-chr6:26198057..26199976,2	MCF-7	breast:

No data

Variant related genes	Relation type
HIST1H3A	TF binding region
HIST1H4A	TF binding region
ENSG00000197409	Chromatin interaction
ENSG00000196866	Chromatin interaction
ENSG00000197846	Chromatin interaction

Extended variants
information (count: 43 )
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];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11751732	0.91[EUR][1000 genomes]
rs11755492	0.97[EUR][1000 genomes]
rs11756400	0.92[EUR][1000 genomes]
rs11756659	0.86[ASN][1000 genomes]
rs11758372	0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs11758378	0.95[EUR][1000 genomes]
rs11759668	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11961143	0.97[EUR][1000 genomes]
rs11965426	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2051538	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2230654	0.91[EUR][1000 genomes]
rs36125084	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs41266783	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs55661658	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs59281021	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61289224	0.91[EUR][1000 genomes]
rs62394537	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs62394540	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62394542	0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62394550	0.92[EUR][1000 genomes]
rs66505449	0.97[EUR][1000 genomes]
rs66536062	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6906460	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6925912	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6935470	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7773526	0.84[EUR][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	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
13	nsv916992	chr6:25991630-26280921	Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1159 gene(s)	inside rSNPs	diseases
14	nsv1028232	chr6:26005449-26319756	Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1171 gene(s)	inside rSNPs	diseases
15	nsv870314	chr6:26008435-26280807	Flanking Active TSS Enhancers Active TSS Genic enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1151 gene(s)	inside rSNPs	diseases
16	nsv1023457	chr6:26014014-26305407	Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1170 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs62000984	TRIM38	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:26001600-26020600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr6:26008800-26020600	Weak transcription	Spleen	Spleen
3	chr6:26016200-26018400	Flanking Active TSS	Fetal Muscle Leg	muscle
4	chr6:26016200-26018600	Active TSS	ES-I3 Cell Line	embryonic stem cell
5	chr6:26016200-26019800	Active TSS	Fetal Kidney	kidney
6	chr6:26016400-26017800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr6:26016400-26017800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr6:26016400-26017800	Flanking Active TSS	Fetal Intestine Small	intestine
9	chr6:26016400-26018000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr6:26016400-26018000	Active TSS	Left Ventricle	heart
11	chr6:26016400-26018000	Active TSS	Right Atrium	heart
12	chr6:26016400-26018200	Active TSS	iPS-18 Cell Line	embryonic stem cell
13	chr6:26016400-26018200	Active TSS	Ovary	ovary
14	chr6:26016400-26018400	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr6:26016400-26018600	Active TSS	iPS-20b Cell Line	embryonic stem cell
16	chr6:26016600-26017800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr6:26016600-26017800	Flanking Active TSS	NHEK	skin
18	chr6:26016600-26017800	Flanking Active TSS	Osteobl	bone
19	chr6:26016600-26018000	Active TSS	Fetal Heart	heart
20	chr6:26016600-26018000	Flanking Active TSS	HUVEC	blood vessel
21	chr6:26016600-26018200	Active TSS	HUES48 Cell Line	embryonic stem cell
22	chr6:26016600-26018200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr6:26016600-26018200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr6:26016600-26018200	Bivalent/Poised TSS	Skeletal Muscle Female	skeletal muscle
25	chr6:26016600-26018200	Flanking Active TSS	HMEC	breast
26	chr6:26016600-26018200	Active TSS	NHDF-Ad	bronchial
27	chr6:26016600-26018400	Active TSS	iPS-15b Cell Line	embryonic stem cell
28	chr6:26016600-26018400	Active TSS	Aorta	Aorta
29	chr6:26016600-26018400	Active TSS	Duodenum Smooth Muscle	Duodenum
30	chr6:26016600-26018600	Active TSS	H9 Cell Line	embryonic stem cell
31	chr6:26016800-26017800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
32	chr6:26016800-26017800	Active TSS	H1 Cell Line	embryonic stem cell
33	chr6:26016800-26017800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr6:26016800-26018000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr6:26016800-26018000	Active TSS	HUES64 Cell Line	embryonic stem cell
36	chr6:26016800-26018000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
37	chr6:26016800-26018200	Active TSS	HUES6 Cell Line	embryonic stem cell
38	chr6:26016800-26018200	Active TSS	Esophagus	oesophagus
39	chr6:26016800-26018400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
40	chr6:26016800-26018400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr6:26017000-26017800	Flanking Active TSS	Fetal Intestine Large	intestine
42	chr6:26017000-26018000	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr6:26017000-26018000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
44	chr6:26017000-26018000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr6:26017000-26018000	Flanking Active TSS	Fetal Thymus	thymus
46	chr6:26017000-26018400	Active TSS	Breast Myoepithelial Primary Cells	Breast
47	chr6:26017000-26018400	Active TSS	Brain Angular Gyrus	brain
48	chr6:26017000-26018600	Active TSS	Fetal Brain Male	brain
49	chr6:26017200-26017800	Enhancers	Primary T killer memory cells from peripheral blood	blood
50	chr6:26017200-26017800	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain

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