Variant report

Variant	rs35546863
Chromosome Location	chr6:106984725-106984726
allele	C/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	NFIC	chr6:106984611-106985079	SK-N-SH	brain:	n/a	n/a
2	GATA3	chr6:106984132-106985320	SK-N-SH	brain:	n/a	n/a
3	ZNF143	chr6:106984722-106985091	GM12878	blood:	n/a	n/a
4	TCF12	chr6:106984109-106985336	SK-N-SH	brain:	n/a	chr6:106984947-106984954
5	EP300	chr6:106984609-106985050	SK-N-SH_RA	brain:	n/a	n/a
6	EP300	chr6:106984318-106985386	SK-N-SH	brain:	n/a	chr6:106985122-106985136
7	GATA3	chr6:106984093-106985341	SK-N-SH	brain:	n/a	n/a
8	MAX	chr6:106984689-106985199	SK-N-SH	brain:	n/a	n/a
9	FOSL2	chr6:106984629-106985040	SK-N-SH	brain:	n/a	n/a
10	TEAD4	chr6:106984467-106985277	SK-N-SH	brain:	n/a	n/a
11	TEAD4	chr6:106984480-106985260	SK-N-SH	brain:	n/a	n/a
12	MAX	chr6:106984718-106985183	SK-N-SH	brain:	n/a	n/a
13	PBX3	chr6:106984182-106985261	SK-N-SH	brain:	n/a	n/a
14	POLR2A	chr6:106984612-106985169	SK-N-SH	brain:	n/a	n/a
15	FOXM1	chr6:106984310-106985369	SK-N-SH	brain:	n/a	n/a
16	EBF1	chr6:106984614-106985133	GM12878	blood:	n/a	n/a
17	RXRA	chr6:106984553-106985178	SK-N-SH	brain:	n/a	chr6:106985029-106985038
18	EP300	chr6:106984393-106985348	SK-N-SH	brain:	n/a	chr6:106985122-106985136
19	EP300	chr6:106984432-106985353	SK-N-SH	brain:	n/a	chr6:106985122-106985136
20	FOXM1	chr6:106984585-106985172	SK-N-SH	brain:	n/a	n/a
21	JUND	chr6:106984122-106985346	SK-N-SH	brain:	n/a	n/a
22	JUND	chr6:106984440-106985170	SK-N-SH	brain:	n/a	n/a
23	JUND	chr6:106984549-106985267	SK-N-SH	brain:	n/a	n/a
24	NFIC	chr6:106984431-106985285	SK-N-SH	brain:	n/a	n/a
25	FOSL2	chr6:106984499-106985293	SK-N-SH	brain:	n/a	n/a
26	EP300	chr6:106984550-106985187	SK-N-SH_RA	brain:	n/a	chr6:106985122-106985136
27	TCF12	chr6:106984013-106985387	SK-N-SH	brain:	n/a	chr6:106984947-106984954
28	PBX3	chr6:106984583-106985167	SK-N-SH	brain:	n/a	n/a
29	POLR2A	chr6:106984707-106987556	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:106982665..106985601-chr6:106993025..106995759,2	MCF-7	breast:
2	chr6:106982668..106985044-chr6:106987673..106989483,2	K562	blood:
3	chr6:106972979..106975776-chr6:106983451..106985409,2	MCF-7	breast:

Variant related genes	Relation type
AIM1	TF binding region
ENSG00000112297	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs1057433	0.86[AMR][1000 genomes]
rs1159148	0.82[ASN][1000 genomes]
rs13193036	0.85[ASN][1000 genomes]
rs13194986	0.82[ASN][1000 genomes]
rs13202166	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13202942	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13207381	0.89[ASN][1000 genomes]
rs13218830	0.82[ASN][1000 genomes]
rs13218960	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13219061	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13220097	0.82[ASN][1000 genomes]
rs17495644	0.89[ASN][1000 genomes]
rs17495720	0.89[ASN][1000 genomes]
rs17560979	0.82[ASN][1000 genomes]
rs1841688	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1841689	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1870866	0.82[ASN][1000 genomes]
rs2297970	0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2306099	0.89[ASN][1000 genomes]
rs2353050	0.85[ASN][1000 genomes]
rs34590393	0.89[ASN][1000 genomes]
rs35090908	0.85[ASN][1000 genomes]
rs35452551	0.85[ASN][1000 genomes]
rs35790766	0.82[ASN][1000 genomes]
rs35843244	0.89[ASN][1000 genomes]
rs55858175	0.82[ASN][1000 genomes]
rs56361614	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72941340	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7740989	0.82[ASN][1000 genomes]
rs7752730	0.82[ASN][1000 genomes]
rs9320173	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9320174	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9320175	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9480681	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9480682	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9486381	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9486382	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9486383	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9486384	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9486385	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9486386	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9486387	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9486388	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	esv3407164	chr6:106982684-106985232	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
5	esv3418513	chr6:106982959-106984957	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
6	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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs35546863	QRSL1	Cis_1M	lymphoblastoid	RTeQTL
rs35546863	QRSL1	cis	Esophagus Muscularis	GTEx
rs35546863	QRSL1	cis	Nerve Tibial	GTEx
rs35546863	QRSL1	cis	Thyroid	GTEx

Chromatin state (count:69 , 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	chr6:106973400-106985600	Weak transcription	Stomach Mucosa	stomach
6	chr6:106973600-106985800	Weak transcription	Thymus	Thymus
7	chr6:106973600-106986000	Genic enhancers	Primary T helper memory cells from peripheral blood 1	blood
8	chr6:106973600-106992800	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr6:106976400-106986200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
10	chr6:106976600-106991400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr6:106977000-106986400	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr6:106978800-106985600	Weak transcription	Fetal Thymus	thymus
13	chr6:106978800-106993800	Weak transcription	NHLF	lung
14	chr6:106979000-107001400	Weak transcription	Pancreas	Pancrea
15	chr6:106979600-106987200	Weak transcription	HepG2	liver
16	chr6:106980800-106986200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr6:106980800-106986400	Strong transcription	Liver	Liver
18	chr6:106981400-106988000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr6:106981600-106995600	Weak transcription	Colonic Mucosa	Colon
20	chr6:106981800-106985200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr6:106981800-106985600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr6:106981800-106985600	Weak transcription	Esophagus	oesophagus
23	chr6:106981800-106987800	Weak transcription	Lung	lung
24	chr6:106982400-106984800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
25	chr6:106982400-106984800	Genic enhancers	NHEK	skin
26	chr6:106982400-106986000	Weak transcription	Placenta	Placenta
27	chr6:106982400-106987400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
28	chr6:106982400-106987600	Genic enhancers	Primary T helper cells PMA-I stimulated	--
29	chr6:106982400-106987800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr6:106982400-107000800	Weak transcription	Rectal Smooth Muscle	rectum
31	chr6:106982600-106985600	Weak transcription	Fetal Intestine Large	intestine
32	chr6:106982600-106987200	Weak transcription	Hela-S3	cervix
33	chr6:106982800-106993200	Weak transcription	HUVEC	blood vessel
34	chr6:106983000-106987800	Weak transcription	Adipose Nuclei	Adipose
35	chr6:106983400-106985000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr6:106983400-106985000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
37	chr6:106983400-106985000	Weak transcription	GM12878-XiMat	blood
38	chr6:106983400-106989000	Weak transcription	Rectal Mucosa Donor 31	rectum
39	chr6:106983400-106989800	Strong transcription	Dnd41	blood
40	chr6:106983600-106985400	Weak transcription	Primary T cells fromperipheralblood	blood
41	chr6:106984000-106985000	Strong transcription	Rectal Mucosa Donor 29	rectum
42	chr6:106984000-106985000	Enhancers	NHDF-Ad	bronchial
43	chr6:106984000-106985200	Enhancers	Duodenum Mucosa	Duodenum
44	chr6:106984000-106986000	Enhancers	Fetal Intestine Small	intestine
45	chr6:106984000-106986800	Genic enhancers	Primary T helper cells fromperipheralblood	blood
46	chr6:106984000-106986800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
47	chr6:106984000-106987800	Genic enhancers	Primary T cells from cord blood	blood
48	chr6:106984000-106989200	Enhancers	Primary monocytes fromperipheralblood	blood
49	chr6:106984200-106984800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
50	chr6:106984200-106984800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin

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