Variant report

Variant	rs6660991
Chromosome Location	chr1:241780207-241780208
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:241778937..241781849-chr1:241955297..241957609,2	K562	blood:
2	chr1:241777588..241780548-chr1:241795040..241796800,2	MCF-7	breast:
3	chr1:241776774..241781436-chr1:241786903..241791805,5	MCF-7	breast:
4	chr1:241778921..241781913-chr1:242009994..242011882,2	K562	blood:

Variant related genes	Relation type
ENSG00000174371	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs12141288	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12141693	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs3753223	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs3765817	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3765819	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3765822	1.00[ASN][1000 genomes]
rs3765827	1.00[ASN][1000 genomes]
rs3819978	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3819979	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4660108	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6674268	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73139006	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73139008	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73139010	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73139033	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv918034	chr1:241072791-242005532	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	32 gene(s)	inside rSNPs	diseases
2	nsv997966	chr1:241100739-242087629	Active TSS Genic enhancers Flanking Active TSS Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	40 gene(s)	inside rSNPs	diseases
3	nsv1002214	chr1:241458939-242099790	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
4	nsv549460	chr1:241494578-241833287	Genic enhancers Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
5	nsv1009579	chr1:241499537-241824631	Bivalent/Poised TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
6	nsv530112	chr1:241522031-241840269	Strong transcription Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
7	nsv873368	chr1:241533392-242195928	Weak transcription Active TSS Transcr. at gene 5' and 3' Enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
8	nsv873372	chr1:241690554-242438293	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
9	nsv427963	chr1:241718799-241832833	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6660991	OPN3	cis	lymphoblastoid	seeQTL

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:241750600-241786000	Weak transcription	Fetal Brain Female	brain
2	chr1:241750800-241786200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr1:241753400-241791200	Weak transcription	Thymus	Thymus
4	chr1:241754400-241782600	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr1:241756000-241791000	Weak transcription	Fetal Thymus	thymus
6	chr1:241758000-241790800	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr1:241758000-241797200	Weak transcription	Left Ventricle	heart
8	chr1:241758000-241800200	Weak transcription	Ovary	ovary
9	chr1:241758800-241802400	Weak transcription	Right Ventricle	heart
10	chr1:241759000-241790600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr1:241764600-241781400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr1:241766200-241798600	Weak transcription	Fetal Muscle Leg	muscle
13	chr1:241767800-241788600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
14	chr1:241767800-241790600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr1:241768000-241787600	Weak transcription	Primary T cells from cord blood	blood
16	chr1:241768000-241791000	Weak transcription	Primary hematopoietic stem cells	blood
17	chr1:241774800-241782200	Weak transcription	Primary B cells from peripheral blood	blood
18	chr1:241775200-241791400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr1:241776400-241784200	Weak transcription	Primary monocytes fromperipheralblood	blood
20	chr1:241776400-241788400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr1:241776400-241790800	Weak transcription	K562	blood
22	chr1:241776400-241791200	Weak transcription	HSMMtube	muscle
23	chr1:241776400-241795000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr1:241776400-241795200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr1:241776400-241795800	Weak transcription	Hela-S3	cervix
26	chr1:241776400-241797400	Weak transcription	NHLF	lung
27	chr1:241776800-241788000	Weak transcription	NHEK	skin
28	chr1:241776800-241790800	Weak transcription	HUVEC	blood vessel
29	chr1:241778200-241780400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr1:241778200-241780600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr1:241778400-241784800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr1:241779200-241790600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr1:241779400-241782400	Weak transcription	Lung	lung
34	chr1:241779400-241782400	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr1:241779400-241783000	Strong transcription	Primary B cells from cord blood	blood
36	chr1:241779400-241783000	Weak transcription	Stomach Mucosa	stomach
37	chr1:241779400-241787200	Weak transcription	Gastric	stomach
38	chr1:241779400-241787400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr1:241779400-241787400	Weak transcription	Colonic Mucosa	Colon
40	chr1:241779400-241787400	Weak transcription	Esophagus	oesophagus
41	chr1:241779400-241790600	Weak transcription	NH-A	brain
42	chr1:241779400-241791400	Weak transcription	HSMM	muscle
43	chr1:241779400-241798600	Weak transcription	Fetal Intestine Large	intestine
44	chr1:241779400-241800400	Weak transcription	Osteobl	bone
45	chr1:241779400-241800600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr1:241779400-241801000	Weak transcription	Fetal Intestine Small	intestine
47	chr1:241779600-241781800	Weak transcription	Rectal Mucosa Donor 31	rectum
48	chr1:241779600-241782800	Weak transcription	Rectal Mucosa Donor 29	rectum
49	chr1:241779600-241786000	Weak transcription	Muscle Satellite Cultured Cells	--
50	chr1:241779600-241787200	Weak transcription	Monocytes-CD14+_RO01746	blood

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