Variant report

Variant	rs783398
Chromosome Location	chr6:106987019-106987020
allele	A/G
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	chr6:106985730-106987594	GM12892	blood:	n/a	n/a
2	GATA3	chr6:106986792-106987023	T-47D	breast:	n/a	n/a
3	POLR2A	chr6:106985434-106987034	GM12892	blood:	n/a	n/a
4	POLR2A	chr6:106987012-106988253	GM12892	blood:	n/a	n/a
5	POLR2A	chr6:106984707-106987556	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:106976336..106978142-chr6:106984891..106987411,2	K562	blood:
2	chr6:106939256..106941678-chr6:106985710..106988008,2	MCF-7	breast:

Variant related genes	Relation type
AIM1	TF binding region

Extended variants
information (count: 13 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs2792466	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4946760	1.00[ASN][1000 genomes]
rs6941640	0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs783390	0.90[ASN][1000 genomes]
rs783392	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs783393	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs783394	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs783397	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs783399	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932155	chr6:106281728-107030467	Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv532047	chr6:106591482-107143252	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	nsv870375	chr6:106696090-107047892	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
4	nsv1017419	chr6:106984669-106997000	Enhancers Strong transcription Flanking Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs783398	QRSL1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:106961000-107001400	Weak transcription	Gastric	stomach
2	chr6:106964800-106991000	Weak transcription	Spleen	Spleen
3	chr6:106964800-107029800	Weak transcription	Small Intestine	intestine
4	chr6:106970600-107022400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr6:106973600-106992800	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr6:106976600-106991400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr6:106978800-106993800	Weak transcription	NHLF	lung
8	chr6:106979000-107001400	Weak transcription	Pancreas	Pancrea
9	chr6:106979600-106987200	Weak transcription	HepG2	liver
10	chr6:106981400-106988000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr6:106981600-106995600	Weak transcription	Colonic Mucosa	Colon
12	chr6:106981800-106987800	Weak transcription	Lung	lung
13	chr6:106982400-106987400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
14	chr6:106982400-106987600	Genic enhancers	Primary T helper cells PMA-I stimulated	--
15	chr6:106982400-106987800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr6:106982400-107000800	Weak transcription	Rectal Smooth Muscle	rectum
17	chr6:106982600-106987200	Weak transcription	Hela-S3	cervix
18	chr6:106982800-106993200	Weak transcription	HUVEC	blood vessel
19	chr6:106983000-106987800	Weak transcription	Adipose Nuclei	Adipose
20	chr6:106983400-106989000	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr6:106983400-106989800	Strong transcription	Dnd41	blood
22	chr6:106984000-106987800	Genic enhancers	Primary T cells from cord blood	blood
23	chr6:106984000-106989200	Enhancers	Primary monocytes fromperipheralblood	blood
24	chr6:106984200-106987200	Enhancers	Primary neutrophils fromperipheralblood	blood
25	chr6:106984400-106987200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr6:106984400-106987800	Genic enhancers	Primary B cells from cord blood	blood
27	chr6:106984400-106990200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr6:106984600-106988600	Enhancers	Primary hematopoietic stem cells	blood
29	chr6:106984800-106989800	Strong transcription	NHEK	skin
30	chr6:106985000-106987800	Strong transcription	GM12878-XiMat	blood
31	chr6:106985000-106988000	Strong transcription	HMEC	breast
32	chr6:106985000-106988200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr6:106985000-106993800	Weak transcription	NH-A	brain
34	chr6:106985400-106988200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
35	chr6:106985600-106988000	Strong transcription	Esophagus	oesophagus
36	chr6:106985800-106988600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr6:106985800-106988800	Weak transcription	Duodenum Mucosa	Duodenum
38	chr6:106985800-107019200	Weak transcription	Aorta	Aorta
39	chr6:106986000-106988200	Enhancers	Placenta	Placenta
40	chr6:106986200-106987400	Genic enhancers	Primary T cells fromperipheralblood	blood
41	chr6:106986200-106992000	Strong transcription	Fetal Intestine Small	intestine
42	chr6:106986200-106993400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr6:106986200-106994000	Weak transcription	Stomach Mucosa	stomach
44	chr6:106986400-106987200	Weak transcription	NHDF-Ad	bronchial
45	chr6:106986400-106987600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr6:106986400-106988000	Weak transcription	Liver	Liver
47	chr6:106986400-106989200	Weak transcription	Fetal Thymus	thymus
48	chr6:106986400-106993000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr6:106986400-106994600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
50	chr6:106986400-106995000	Weak transcription	Thymus	Thymus

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