Variant report

Variant	rs7648424
Chromosome Location	chr3:150423391-150423392
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:150320068..150322587-chr3:150419780..150423653,7	MCF-7	breast:
2	chr3:150419019..150423394-chr3:150479448..150481415,4	MCF-7	breast:
3	chr3:150421205..150424923-chr3:150480120..150484463,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000181788	Chromatin interaction
ENSG00000198843	Chromatin interaction
ENSG00000244265	Chromatin interaction
ENSG00000120742	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1131685	0.84[ASN][1000 genomes]
rs12494272	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12630292	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12634699	0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12638096	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13074103	0.84[ASN][1000 genomes]
rs13074670	0.84[ASN][1000 genomes]
rs13086267	0.80[ASN][1000 genomes]
rs13086869	0.83[ASN][1000 genomes]
rs13090897	0.84[ASN][1000 genomes]
rs16862794	0.88[CHD][hapmap]
rs17281287	0.83[ASN][1000 genomes]
rs1897489	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1897491	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1897494	0.84[ASN][1000 genomes]
rs28460384	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28790675	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4558804	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55838848	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs57680627	0.81[ASN][1000 genomes]
rs6766333	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6784407	0.92[CEU][hapmap];0.83[CHB][hapmap];0.86[JPT][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7641475	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7650706	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.87[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9682958	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9814796	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9848451	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9858987	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9869495	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9876621	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532662	chr3:150180747-150633414	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	101 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7648424	SELT	cis	parietal	SCAN

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:150422000-150430400	Weak transcription	Spleen	Spleen
2	chr3:150422200-150423600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
3	chr3:150422200-150423800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
4	chr3:150422200-150428000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr3:150422200-150428200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr3:150422200-150429800	Weak transcription	Pancreas	Pancrea
7	chr3:150422200-150439400	Weak transcription	Ovary	ovary
8	chr3:150422200-150443200	Weak transcription	Lung	lung
9	chr3:150422400-150423400	Enhancers	Primary T helper cells fromperipheralblood	blood
10	chr3:150422400-150423400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
11	chr3:150422400-150424400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr3:150422400-150425000	Weak transcription	Fetal Lung	lung
13	chr3:150422400-150425400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr3:150422400-150426200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr3:150422400-150427000	Weak transcription	Fetal Intestine Large	intestine
16	chr3:150422400-150427200	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr3:150422400-150428200	Weak transcription	Brain Anterior Caudate	brain
18	chr3:150422400-150428600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr3:150422400-150429800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr3:150422400-150430000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr3:150422400-150434800	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr3:150422400-150443000	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr3:150422600-150423400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
24	chr3:150422600-150423600	Enhancers	Fetal Kidney	kidney
25	chr3:150422600-150423800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr3:150422600-150423800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr3:150422600-150425200	Weak transcription	Primary T cells from cord blood	blood
28	chr3:150422600-150425400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr3:150422600-150425600	Weak transcription	Primary B cells from cord blood	blood
30	chr3:150422600-150425600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
31	chr3:150422600-150425600	Weak transcription	A549	lung
32	chr3:150422600-150426000	Weak transcription	Fetal Muscle Leg	muscle
33	chr3:150422600-150426000	Weak transcription	Fetal Thymus	thymus
34	chr3:150422600-150426800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
35	chr3:150422600-150427600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr3:150422600-150427600	Weak transcription	Fetal Stomach	stomach
37	chr3:150422600-150427800	Weak transcription	Left Ventricle	heart
38	chr3:150422600-150428000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr3:150422600-150428200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr3:150422600-150428200	Weak transcription	Aorta	Aorta
41	chr3:150422600-150428200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr3:150422600-150428200	Weak transcription	Osteobl	bone
43	chr3:150422600-150428600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr3:150422600-150429800	Weak transcription	Placenta	Placenta
45	chr3:150422600-150429800	Weak transcription	Thymus	Thymus
46	chr3:150422600-150431000	Weak transcription	Cortex derived primary cultured neurospheres	brain
47	chr3:150422600-150439200	Weak transcription	Primary B cells from peripheral blood	blood
48	chr3:150422600-150439200	Weak transcription	Fetal Intestine Small	intestine
49	chr3:150422600-150439400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr3:150422600-150439400	Weak transcription	Adipose Nuclei	Adipose

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