Variant report

Variant	rs587640
Chromosome Location	chr1:241790148-241790149
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:241789367..241790948-chr1:241857642..241860164,2	K562	blood:
2	chr1:241789486..241791019-chr1:241984145..241986452,2	K562	blood:
3	chr1:241693395..241696373-chr1:241788082..241790840,3	K562	blood:
4	chr1:241789280..241791563-chr1:241817255..241819407,2	K562	blood:
5	chr1:241692639..241698024-chr1:241788169..241793747,6	K562	blood:
6	chr1:241776774..241781436-chr1:241786903..241791805,5	MCF-7	breast:
7	chr1:241788460..241791197-chr1:241796744..241798499,2	MCF-7	breast:
8	chr1:241693845..241695449-chr1:241789747..241792486,2	MCF-7	breast:
9	chr1:241788295..241791166-chr1:242001121..242003916,2	K562	blood:
10	chr1:241788676..241790229-chr1:242053556..242055267,2	K562	blood:
11	chr1:241787560..241792499-chr1:241801954..241804865,6	MCF-7	breast:
12	chr1:241789329..241791723-chr1:241798854..241801154,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000117009	Chromatin interaction
ENSG00000203668	Chromatin interaction
ENSG00000054277	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs2756224	0.94[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.84[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3765821	0.91[JPT][hapmap]
rs584695	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs593963	0.91[CEU][hapmap];0.92[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.87[TSI][hapmap];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs614251	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs622726	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs624385	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs628720	0.95[CEU][hapmap];0.84[TSI][hapmap];0.82[EUR][1000 genomes]
rs631143	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]
rs652571	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs676750	1.00[CEU][hapmap];0.93[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.98[TSI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs680382	0.86[AFR][1000 genomes]
rs684338	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs688659	0.94[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.95[TSI][hapmap];0.81[YRI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7513575	0.86[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs587640	CHML	cis	cerebellum	SCAN
rs587640	OPN3	cis	cerebellum	SCAN

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:241753400-241791200	Weak transcription	Thymus	Thymus
2	chr1:241756000-241791000	Weak transcription	Fetal Thymus	thymus
3	chr1:241758000-241790800	Weak transcription	HUES64 Cell Line	embryonic stem cell
4	chr1:241758000-241797200	Weak transcription	Left Ventricle	heart
5	chr1:241758000-241800200	Weak transcription	Ovary	ovary
6	chr1:241758800-241802400	Weak transcription	Right Ventricle	heart
7	chr1:241759000-241790600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr1:241766200-241798600	Weak transcription	Fetal Muscle Leg	muscle
9	chr1:241767800-241790600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr1:241768000-241791000	Weak transcription	Primary hematopoietic stem cells	blood
11	chr1:241775200-241791400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr1:241776400-241790800	Weak transcription	K562	blood
13	chr1:241776400-241791200	Weak transcription	HSMMtube	muscle
14	chr1:241776400-241795000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr1:241776400-241795200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr1:241776400-241795800	Weak transcription	Hela-S3	cervix
17	chr1:241776400-241797400	Weak transcription	NHLF	lung
18	chr1:241776800-241790800	Weak transcription	HUVEC	blood vessel
19	chr1:241779200-241790600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr1:241779400-241790600	Weak transcription	NH-A	brain
21	chr1:241779400-241791400	Weak transcription	HSMM	muscle
22	chr1:241779400-241798600	Weak transcription	Fetal Intestine Large	intestine
23	chr1:241779400-241800400	Weak transcription	Osteobl	bone
24	chr1:241779400-241800600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr1:241779400-241801000	Weak transcription	Fetal Intestine Small	intestine
26	chr1:241779600-241790800	Weak transcription	HMEC	breast
27	chr1:241779600-241796600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr1:241779800-241795200	Weak transcription	Placenta	Placenta
29	chr1:241781200-241799800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr1:241783400-241798000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr1:241783800-241791200	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr1:241784000-241791200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr1:241784200-241791000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
34	chr1:241784400-241800600	Weak transcription	Fetal Brain Male	brain
35	chr1:241785200-241798800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr1:241785400-241797200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr1:241786200-241800400	Weak transcription	Psoas Muscle	Psoas
38	chr1:241786400-241791400	Weak transcription	Brain Germinal Matrix	brain
39	chr1:241786600-241790800	Weak transcription	Adipose Nuclei	Adipose
40	chr1:241786600-241790800	Weak transcription	Liver	Liver
41	chr1:241786600-241800800	Weak transcription	Cortex derived primary cultured neurospheres	brain
42	chr1:241786800-241790600	Weak transcription	Muscle Satellite Cultured Cells	--
43	chr1:241786800-241790800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
44	chr1:241786800-241796200	Weak transcription	Fetal Brain Female	brain
45	chr1:241787400-241791200	Weak transcription	HUES48 Cell Line	embryonic stem cell
46	chr1:241787600-241797200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr1:241787800-241802400	Weak transcription	Fetal Muscle Trunk	muscle
48	chr1:241788000-241790600	Strong transcription	Primary B cells from cord blood	blood
49	chr1:241788000-241790600	Weak transcription	A549	lung
50	chr1:241788000-241792000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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