Variant report

Variant	rs7615865
Chromosome Location	chr3:151073033-151073034
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 47 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10755105	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs10935838	0.93[ASN][1000 genomes]
rs11922647	0.88[ASN][1000 genomes]
rs1352887	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1388619	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1388622	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1388623	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1388624	0.92[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1388626	0.93[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs1466684	0.93[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs1491978	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1491979	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1491980	0.93[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1491981	0.93[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs1873622	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2046934	0.93[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2172249	0.96[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2870517	0.86[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap]
rs3732762	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3732764	0.92[CEU][hapmap];0.93[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.97[TSI][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3821667	0.93[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs3971191	0.93[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs3975401	0.92[ASN][1000 genomes]
rs3975403	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3975404	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs4146770	0.86[JPT][hapmap]
rs4679802	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs4680374	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs6440731	0.86[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs6440732	0.86[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs6763983	0.84[ASN][1000 genomes]
rs6769397	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs6782212	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6790748	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs6794283	1.00[YRI][hapmap]
rs6809388	0.92[JPT][hapmap]
rs6809705	0.85[JPT][hapmap]
rs7611328	0.86[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap]
rs7620353	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs7621876	0.93[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs7633362	0.93[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs9820422	0.93[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs9877389	0.93[CHB][hapmap];0.89[CHD][hapmap];0.86[JPT][hapmap];0.93[ASN][1000 genomes]
rs9878459	0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv460894	chr3:150770614-151095093	Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv592045	chr3:150770614-151095093	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv829757	chr3:151044880-151226442	Enhancers Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7615865	CLRN1	cis	parietal	SCAN

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:151063800-151099800	Weak transcription	Fetal Intestine Small	intestine
2	chr3:151064400-151089200	Weak transcription	NHLF	lung
3	chr3:151064600-151075200	Weak transcription	Adipose Nuclei	Adipose
4	chr3:151064600-151112400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr3:151065400-151079600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr3:151065600-151109400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr3:151065600-151115200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr3:151065800-151082200	Weak transcription	Fetal Thymus	thymus
9	chr3:151066000-151074800	Weak transcription	Brain Anterior Caudate	brain
10	chr3:151066400-151075000	Weak transcription	Brain Hippocampus Middle	brain
11	chr3:151066800-151074600	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr3:151067800-151083600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr3:151068000-151075000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr3:151068000-151078800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr3:151068000-151079600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr3:151068000-151082600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr3:151068200-151073600	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr3:151068400-151075000	Weak transcription	Aorta	Aorta
19	chr3:151068600-151073800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr3:151069200-151073400	Weak transcription	HUES64 Cell Line	embryonic stem cell
21	chr3:151069200-151078800	Weak transcription	HUES48 Cell Line	embryonic stem cell
22	chr3:151069200-151078800	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr3:151069400-151129800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr3:151069800-151073600	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr3:151070400-151082800	Weak transcription	Primary hematopoietic stem cells	blood
26	chr3:151070600-151075000	Weak transcription	Primary B cells from peripheral blood	blood
27	chr3:151070800-151075000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
28	chr3:151071000-151074400	Weak transcription	Primary B cells from cord blood	blood
29	chr3:151071400-151073600	Weak transcription	Primary monocytes fromperipheralblood	blood
30	chr3:151071400-151073600	Weak transcription	Primary neutrophils fromperipheralblood	blood
31	chr3:151071400-151073600	Weak transcription	Monocytes-CD14+_RO01746	blood
32	chr3:151072400-151080200	Weak transcription	Placenta	Placenta
33	chr3:151072400-151089800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr3:151072400-151091400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr3:151072600-151099800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr3:151072800-151075000	Weak transcription	Fetal Brain Female	brain

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