Variant report

Variant	rs6680866
Chromosome Location	chr1:152022989-152022990
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:0)
Chromatin interactive
region (count:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:4 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	JUND	chr1:152019837-152022990	Hela-S3	cervix:	n/a	chr1:152020041-152020051 chr1:152021190-152021202 chr1:152020042-152020050 chr1:152020740-152020749 chr1:152020738-152020749 chr1:152020040-152020052
2	POLR2A	chr1:152018724-152024242	MCF10A-Er-Src	breast:	n/a	n/a
3	SMARCC2	chr1:152022306-152024242	Hela-S3	cervix:	n/a	n/a
4	SMARCC1	chr1:152022801-152024146	Hela-S3	cervix:	n/a	n/a

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:152021342..152023033-chr1:210545433..210547102,2	MCF-7	breast:
2	chr1:152022027..152023625-chr1:152154015..152156299,2	MCF-7	breast:
3	chr1:151880510..151884478-chr1:152021819..152026164,4	MCF-7	breast:
4	chr1:152021494..152023021-chr1:152123294..152125529,2	MCF-7	breast:
5	chr1:152021831..152023817-chr1:152026030..152027849,2	K562	blood:
6	chr1:151974328..151976089-chr1:152021628..152023753,2	MCF-7	breast:
7	chr1:152021638..152025256-chr1:152144689..152147457,3	MCF-7	breast:
8	chr1:152020471..152023395-chr1:152032705..152034549,2	MCF-7	breast:
9	chr1:152020825..152023230-chr1:152081998..152084966,2	MCF-7	breast:
10	chr1:152003076..152005594-chr1:152022985..152024993,2	K562	blood:
11	chr1:152021534..152023365-chr1:152139804..152141788,2	MCF-7	breast:
12	chr1:152004094..152009269-chr1:152022985..152027910,7	K562	blood:
13	chr1:151961745..151973594-chr1:152015769..152025096,31	MCF-7	breast:

No data

Variant related genes	Relation type
S100A11	TF binding region
ENSG00000237975	Chromatin interaction
ENSG00000197747	Chromatin interaction
ENSG00000159445	Chromatin interaction
ENSG00000229021	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs10494274	1.00[CEU][hapmap];0.89[CHB][hapmap];0.82[JPT][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11582331	1.00[CEU][hapmap];1.00[MKK][hapmap];0.86[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1845792	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1979637	0.85[CEU][hapmap];0.82[TSI][hapmap]
rs4525041	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6682710	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007097	chr1:151832796-152227977	Strong transcription Genic enhancers Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	196 gene(s)	inside rSNPs	diseases
2	nsv1012327	chr1:151835544-152200890	Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	196 gene(s)	inside rSNPs	diseases
3	nsv535159	chr1:151835544-152200890	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Genic enhancers Strong transcription 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 miRNA target site	196 gene(s)	inside rSNPs	diseases
4	nsv872441	chr1:151850072-152034430	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	191 gene(s)	inside rSNPs	diseases
5	nsv547853	chr1:152008671-152236760	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs6680866	SLC39A1	cis	parietal	SCAN
rs6680866	S100A10	cis	parietal	SCAN
rs6680866	LCE3E	cis	parietal	SCAN
rs6680866	FLG-AS1	cis	Thyroid	GTEx
rs6680866	SCNM1	cis	parietal	SCAN
rs6680866	S100A8	cis	parietal	SCAN
rs6680866	THEM5	cis	cerebellum	SCAN
rs6680866	ADAMTSL4	cis	cerebellum	SCAN
rs6680866	S100A10	cis	cerebellum	SCAN
rs6680866	S100A10	cis	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:152021000-152023800	Weak transcription	Fetal Kidney	kidney
2	chr1:152021000-152024200	Enhancers	Fetal Intestine Small	intestine
3	chr1:152021000-152024200	Enhancers	Stomach Mucosa	stomach
4	chr1:152021000-152025200	Weak transcription	Brain Hippocampus Middle	brain
5	chr1:152021200-152023000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr1:152021200-152023000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr1:152021200-152023000	Weak transcription	Esophagus	oesophagus
8	chr1:152021200-152023600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr1:152021200-152023600	Weak transcription	Fetal Thymus	thymus
10	chr1:152021200-152024000	Enhancers	Fetal Intestine Large	intestine
11	chr1:152021200-152024200	Enhancers	Primary hematopoietic stem cells short term culture	blood
12	chr1:152021200-152024200	Enhancers	Muscle Satellite Cultured Cells	--
13	chr1:152021200-152024200	Enhancers	Placenta Amnion	Placenta Amnion
14	chr1:152021200-152024200	Enhancers	NHDF-Ad	bronchial
15	chr1:152021200-152024600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr1:152021200-152024600	Enhancers	Osteobl	bone
17	chr1:152021200-152025200	Enhancers	Primary monocytes fromperipheralblood	blood
18	chr1:152021200-152025200	Enhancers	HMEC	breast
19	chr1:152021200-152025400	Weak transcription	Colonic Mucosa	Colon
20	chr1:152021400-152023000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr1:152021400-152023000	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr1:152021400-152023200	Weak transcription	NHLF	lung
23	chr1:152021400-152023800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr1:152021400-152024000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr1:152021400-152024000	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr1:152021400-152024200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr1:152021400-152024200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr1:152021400-152024400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr1:152021400-152024400	Enhancers	A549	lung
30	chr1:152021400-152025000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr1:152021400-152025000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
32	chr1:152021400-152025000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr1:152021400-152025200	Enhancers	NHEK	skin
34	chr1:152021600-152023000	Weak transcription	Primary B cells from cord blood	blood
35	chr1:152021600-152023000	Enhancers	Hela-S3	cervix
36	chr1:152021600-152023200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr1:152021600-152023400	Weak transcription	K562	blood
38	chr1:152021600-152023600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
39	chr1:152021600-152023600	Weak transcription	Placenta	Placenta
40	chr1:152021600-152023600	Weak transcription	HSMMtube	muscle
41	chr1:152021600-152023800	Weak transcription	Primary T helper cells PMA-I stimulated	--
42	chr1:152021600-152024800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr1:152021600-152024800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
44	chr1:152021800-152023800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
45	chr1:152021800-152025000	Weak transcription	Primary T cells fromperipheralblood	blood
46	chr1:152022000-152025400	Weak transcription	Pancreatic Islets	Pancreatic Islet
47	chr1:152022200-152023000	Weak transcription	Duodenum Mucosa	Duodenum
48	chr1:152022600-152023400	Weak transcription	Small Intestine	intestine
49	chr1:152022800-152023600	Enhancers	Breast Myoepithelial Primary Cells	Breast
50	chr1:152022800-152024000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood

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