Variant report

Variant	rs817534
Chromosome Location	chr2:33473564-33473565
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	chr2:33430736..33432934-chr2:33471410..33474169,2	MCF-7	breast:

Extended variants
information (count: 52 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10169788	0.88[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.94[YRI][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10175557	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10175619	0.84[CEU][hapmap];0.83[AMR][1000 genomes]
rs11124313	0.93[ASW][hapmap];0.92[CEU][hapmap];0.91[CHB][hapmap];0.82[CHD][hapmap];0.90[GIH][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.95[TSI][hapmap];0.94[YRI][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11673950	0.92[CEU][hapmap];0.91[CHB][hapmap];0.88[JPT][hapmap];0.88[YRI][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11684829	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13391131	0.92[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.88[YRI][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13392154	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13394195	0.88[CEU][hapmap];0.94[YRI][hapmap];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17582516	0.92[CEU][hapmap];0.91[CHB][hapmap];0.88[JPT][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2603361	0.89[CEU][hapmap];0.91[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3754829	0.82[GIH][hapmap]
rs3769540	0.96[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3769542	0.83[YRI][hapmap]
rs3769544	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3769545	0.82[CHD][hapmap]
rs41464348	0.88[MEX][hapmap]
rs4233909	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4670387	0.93[ASW][hapmap];0.92[CEU][hapmap];0.91[CHB][hapmap];0.93[GIH][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.98[TSI][hapmap];0.94[YRI][hapmap];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4670408	0.92[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];0.90[GIH][hapmap];0.88[JPT][hapmap];0.96[MEX][hapmap];0.85[MKK][hapmap];0.93[TSI][hapmap];0.88[YRI][hapmap];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62148881	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62148882	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62148927	0.85[AMR][1000 genomes]
rs6543704	0.93[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];0.90[GIH][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.98[TSI][hapmap];0.94[YRI][hapmap];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6543705	0.86[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.81[TSI][hapmap];0.94[YRI][hapmap];0.91[AMR][1000 genomes]
rs6711027	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6739030	0.92[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.88[YRI][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6739506	0.93[ASW][hapmap];0.92[CEU][hapmap];0.91[CHB][hapmap];0.82[CHD][hapmap];0.93[GIH][hapmap];0.88[JPT][hapmap];0.96[MEX][hapmap];0.91[MKK][hapmap];0.95[TSI][hapmap];0.94[YRI][hapmap];0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6739725	0.86[AMR][1000 genomes]
rs711234	0.91[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs711235	0.91[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs723043	0.85[CEU][hapmap];0.82[CHD][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes]
rs749454	1.00[CHB][hapmap]
rs7565095	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7575377	0.88[MEX][hapmap]
rs7586227	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7590205	0.93[ASW][hapmap];0.88[CEU][hapmap];0.82[CHB][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];0.87[MEX][hapmap];0.88[MKK][hapmap];0.98[TSI][hapmap];0.82[YRI][hapmap];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7605474	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs817529	0.93[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.92[LWK][hapmap];0.91[MEX][hapmap];0.94[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs817532	1.00[CEU][hapmap];0.90[CHB][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];0.92[MEX][hapmap];0.83[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs817535	0.87[CHD][hapmap];0.82[GIH][hapmap];0.87[MEX][hapmap]
rs817536	0.93[ASW][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.91[MEX][hapmap];0.84[TSI][hapmap];0.94[YRI][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs817537	0.91[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.84[TSI][hapmap];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs817539	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs877672	0.84[MEX][hapmap]
rs9308934	0.88[JPT][hapmap];0.81[YRI][hapmap]
rs935996	0.83[MEX][hapmap]
rs971793	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv998167	chr2:33074313-33541100	Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
2	nsv535623	chr2:33074313-33541100	Genic enhancers Enhancers Weak transcription Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
3	nsv1005435	chr2:33136117-33747159	Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
4	nsv535624	chr2:33136117-33747159	Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs817534	CLIP4	cis	cerebellum	SCAN

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:33403800-33489800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:33449400-33475400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr2:33466400-33497400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr2:33466600-33500800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr2:33466800-33491200	Weak transcription	Right Ventricle	heart
6	chr2:33467800-33474000	Weak transcription	Fetal Heart	heart
7	chr2:33467800-33475600	Weak transcription	Stomach Smooth Muscle	stomach
8	chr2:33468200-33475800	Weak transcription	Ovary	ovary
9	chr2:33468200-33491000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr2:33468600-33475600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr2:33468600-33475600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr2:33468600-33477000	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr2:33468800-33475400	Weak transcription	NHLF	lung
14	chr2:33469200-33475600	Weak transcription	Fetal Stomach	stomach
15	chr2:33469800-33475800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr2:33469800-33476000	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr2:33469800-33486200	Weak transcription	NHDF-Ad	bronchial
18	chr2:33470400-33479400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr2:33471200-33480800	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr2:33471400-33475600	Weak transcription	Fetal Muscle Leg	muscle
21	chr2:33471800-33491200	Weak transcription	Pancreas	Pancrea
22	chr2:33472000-33475200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr2:33472000-33475800	Weak transcription	Left Ventricle	heart
24	chr2:33472000-33478000	Weak transcription	Liver	Liver
25	chr2:33472000-33489800	Weak transcription	A549	lung
26	chr2:33472000-33491200	Weak transcription	Brain Substantia Nigra	brain
27	chr2:33472000-33516600	Weak transcription	Psoas Muscle	Psoas
28	chr2:33472200-33473800	Weak transcription	Osteobl	bone
29	chr2:33472200-33475600	Weak transcription	Aorta	Aorta
30	chr2:33472200-33476000	Weak transcription	Fetal Muscle Trunk	muscle
31	chr2:33472400-33475600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr2:33472400-33476800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr2:33472400-33491000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
34	chr2:33472600-33492800	Weak transcription	Colon Smooth Muscle	Colon
35	chr2:33473200-33473600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr2:33473200-33477200	Weak transcription	NH-A	brain
37	chr2:33473200-33486600	Weak transcription	Fetal Lung	lung

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