Variant report

Variant	rs631143
Chromosome Location	chr1:241799538-241799539
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:5)
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	BHLHE40	chr1:241798928-241799581	GM12878	blood:	n/a	n/a
2	SPI1	chr1:241798839-241799615	GM12878	blood:	n/a	n/a
3	POLR2A	chr1:241799353-241805428	MCF10A-Er-Src	breast:	n/a	n/a
4	POLR2A	chr1:241799431-241799697	MCF10A-Er-Src	breast:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:241681612..241683346-chr1:241799468..241801013,2	K562	blood:
2	chr1:241798094..241801033-chr1:242010173..242012572,2	MCF-7	breast:
3	chr1:241799429..241802453-chr1:241804405..241808572,4	MCF-7	breast:
4	chr1:241796724..241805103-chr1:242008052..242013159,15	K562	blood:
5	chr1:241799259..241801184-chr1:241862624..241865531,2	K562	blood:

No data

Variant related genes	Relation type
CHML	TF binding region
ENSG00000174371	Chromatin interaction
ENSG00000091483	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs2756224	0.88[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.85[TSI][hapmap];0.91[YRI][hapmap];0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3765821	0.82[JPT][hapmap]
rs584695	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs587640	0.94[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.92[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.95[TSI][hapmap];0.91[YRI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs593963	0.87[CEU][hapmap];0.92[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];0.92[JPT][hapmap];0.94[MEX][hapmap];0.82[TSI][hapmap];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs614251	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs622726	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs624385	0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs628720	0.91[CEU][hapmap];0.89[TSI][hapmap];0.85[EUR][1000 genomes]
rs652571	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs676750	0.95[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.89[MEX][hapmap];0.98[TSI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs684338	0.95[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs688659	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7513451	0.82[EUR][1000 genomes]
rs7513575	0.88[EUR][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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs631143	OPN3	cis	cerebellum	SCAN
rs631143	CHML	cis	cerebellum	SCAN
rs631143	OPN3	cis	multi-tissue	Pritchard

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:241758000-241800200	Weak transcription	Ovary	ovary
2	chr1:241758800-241802400	Weak transcription	Right Ventricle	heart
3	chr1:241779400-241800400	Weak transcription	Osteobl	bone
4	chr1:241779400-241800600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr1:241779400-241801000	Weak transcription	Fetal Intestine Small	intestine
6	chr1:241781200-241799800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr1:241784400-241800600	Weak transcription	Fetal Brain Male	brain
8	chr1:241786200-241800400	Weak transcription	Psoas Muscle	Psoas
9	chr1:241786600-241800800	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr1:241787800-241802400	Weak transcription	Fetal Muscle Trunk	muscle
11	chr1:241788200-241800800	Weak transcription	Gastric	stomach
12	chr1:241788200-241801400	Weak transcription	Colonic Mucosa	Colon
13	chr1:241788200-241802800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr1:241788200-241802800	Weak transcription	Esophagus	oesophagus
15	chr1:241789200-241802800	Weak transcription	Pancreas	Pancrea
16	chr1:241791000-241799600	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr1:241791600-241800200	Weak transcription	Fetal Kidney	kidney
18	chr1:241791600-241800600	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr1:241791600-241800800	Weak transcription	NHDF-Ad	bronchial
20	chr1:241791600-241801400	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr1:241791600-241802200	Weak transcription	Adipose Nuclei	Adipose
22	chr1:241791600-241802200	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr1:241791600-241802400	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr1:241791800-241800600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr1:241791800-241800800	Weak transcription	Primary neutrophils fromperipheralblood	blood
26	chr1:241791800-241801000	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr1:241791800-241801800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
28	chr1:241791800-241802200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr1:241791800-241802400	Weak transcription	Skeletal Muscle Female	skeletal muscle
30	chr1:241792000-241799600	Weak transcription	Primary T helper cells PMA-I stimulated	--
31	chr1:241792000-241801000	Weak transcription	Primary T cells fromperipheralblood	blood
32	chr1:241792600-241799600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
33	chr1:241792800-241800800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr1:241794800-241800200	Strong transcription	K562	blood
35	chr1:241795400-241799800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
36	chr1:241795600-241800200	Weak transcription	Pancreatic Islets	Pancreatic Islet
37	chr1:241795800-241799600	Strong transcription	Hela-S3	cervix
38	chr1:241795800-241799800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
39	chr1:241795800-241799800	Weak transcription	Fetal Stomach	stomach
40	chr1:241796200-241800200	Strong transcription	HUES64 Cell Line	embryonic stem cell
41	chr1:241796400-241799600	Weak transcription	Brain Angular Gyrus	brain
42	chr1:241796600-241800400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
43	chr1:241796600-241800600	Strong transcription	HUES6 Cell Line	embryonic stem cell
44	chr1:241796800-241800600	Strong transcription	HUES48 Cell Line	embryonic stem cell
45	chr1:241797200-241800600	Weak transcription	Aorta	Aorta
46	chr1:241797200-241802400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr1:241797400-241799600	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr1:241797400-241799600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
49	chr1:241797600-241799600	ZNF genes & repeats	Fetal Brain Female	brain
50	chr1:241797600-241799600	Strong transcription	A549	lung

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