Variant report

Variant	rs7645665
Chromosome Location	chr3:150806332-150806333
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:150802084..150805067-chr3:150805477..150808143,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000144893	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs1003246	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1005726	0.94[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.93[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10755104	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs10935825	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.83[GIH][hapmap];0.93[JPT][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10935826	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10935827	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs10935828	1.00[CEU][hapmap];0.92[TSI][hapmap];0.89[EUR][1000 genomes]
rs11914598	0.89[CEU][hapmap];0.88[TSI][hapmap]
rs11919212	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12489984	0.83[EUR][1000 genomes]
rs1431492	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1431493	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs16863172	1.00[CEU][hapmap];0.83[GIH][hapmap];0.92[TSI][hapmap];0.85[EUR][1000 genomes]
rs1835668	1.00[CEU][hapmap];0.92[TSI][hapmap];0.84[EUR][1000 genomes]
rs1897296	0.89[CEU][hapmap];0.83[GIH][hapmap]
rs1920392	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.93[JPT][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2014240	1.00[CEU][hapmap];0.92[TSI][hapmap];0.88[EUR][1000 genomes]
rs2060081	0.94[CEU][hapmap];0.90[CHB][hapmap];0.86[CHD][hapmap];0.93[GIH][hapmap];0.93[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs28594277	0.85[AMR][1000 genomes]
rs3773615	0.94[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.93[GIH][hapmap];0.93[JPT][hapmap];0.82[MEX][hapmap];0.96[TSI][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3915228	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];0.93[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs58990954	0.83[ASN][1000 genomes]
rs61184267	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6414377	1.00[CEU][hapmap];0.83[GIH][hapmap];0.92[TSI][hapmap];0.88[EUR][1000 genomes]
rs6440721	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6765294	0.94[CEU][hapmap];0.86[CHB][hapmap];0.87[JPT][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6767918	1.00[CEU][hapmap];0.92[TSI][hapmap];0.83[EUR][1000 genomes]
rs6772640	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs6780120	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6787683	1.00[CEU][hapmap];0.92[TSI][hapmap];0.83[EUR][1000 genomes]
rs6790661	0.83[EUR][1000 genomes]
rs6801591	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6809388	0.89[CEU][hapmap]
rs6809705	0.89[CEU][hapmap];0.80[MEX][hapmap];0.84[TSI][hapmap];0.82[AMR][1000 genomes]
rs7427471	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs747205	0.83[EUR][1000 genomes]
rs7633492	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9289832	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9683109	1.00[CEU][hapmap];0.92[TSI][hapmap];0.83[EUR][1000 genomes]
rs9813224	0.81[EUR][1000 genomes]
rs9822304	0.87[EUR][1000 genomes]
rs9823077	0.94[CEU][hapmap];0.90[CHB][hapmap];0.93[JPT][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9829728	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs9848163	0.86[EUR][1000 genomes]
rs9850016	0.85[CHB][hapmap];0.86[JPT][hapmap]
rs9876500	0.94[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv915879	chr3:150607390-150860207	Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv829756	chr3:150692636-150889738	Weak transcription Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	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
4	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
5	esv2753152	chr3:150773248-150810545	Bivalent/Poised TSS Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	esv2757897	chr3:150791625-150957485	ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	esv2759188	chr3:150791625-150957485	Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv877648	chr3:150792444-150895145	Enhancers Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7645665	CLRN1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:150802600-150806600	Active TSS	Brain Angular Gyrus	brain
2	chr3:150802600-150806600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
3	chr3:150802600-150806800	Active TSS	Brain Cingulate Gyrus	brain
4	chr3:150803000-150806400	Active TSS	Brain Anterior Caudate	brain
5	chr3:150803000-150806600	Active TSS	Brain Inferior Temporal Lobe	brain
6	chr3:150805200-150806400	Flanking Active TSS	Primary hematopoietic stem cells	blood
7	chr3:150805200-150807400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr3:150805200-150807600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr3:150805200-150808200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr3:150805400-150806800	Enhancers	Primary neutrophils fromperipheralblood	blood
11	chr3:150805400-150806800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr3:150805400-150807600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr3:150805400-150812000	Weak transcription	Thymus	Thymus
14	chr3:150805600-150806800	Enhancers	Dnd41	blood
15	chr3:150805600-150809000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr3:150805600-150811400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr3:150805600-150811600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr3:150805800-150806600	Enhancers	Primary hematopoietic stem cells short term culture	blood
19	chr3:150805800-150809000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr3:150805800-150809800	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr3:150805800-150811200	Weak transcription	Fetal Intestine Small	intestine
22	chr3:150806000-150806400	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
23	chr3:150806000-150806600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr3:150806000-150806600	Active TSS	Fetal Brain Female	brain
25	chr3:150806000-150806800	Enhancers	ES-I3 Cell Line	embryonic stem cell
26	chr3:150806000-150807200	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr3:150806000-150808400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr3:150806000-150809400	Weak transcription	Brain Hippocampus Middle	brain
29	chr3:150806000-150814400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
30	chr3:150806200-150806400	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
31	chr3:150806200-150806400	Enhancers	HUES64 Cell Line	embryonic stem cell
32	chr3:150806200-150806600	Enhancers	Brain Germinal Matrix	brain
33	chr3:150806200-150806800	Enhancers	Cortex derived primary cultured neurospheres	brain
34	chr3:150806200-150806800	Enhancers	Fetal Muscle Leg	muscle
35	chr3:150806200-150807400	Weak transcription	Fetal Brain Male	brain
36	chr3:150806200-150809600	Weak transcription	H1 Cell Line	embryonic stem cell

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