Variant report

Variant	rs4681297
Chromosome Location	chr3:145838895-145838896
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:145829569..145840903-chr3:145873254..145880972,31	MCF-7	breast:

Variant related genes	Relation type
ENSG00000152952	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10935601	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10935602	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10935604	1.00[CEU][hapmap];0.92[CHB][hapmap];0.94[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10935606	0.82[JPT][hapmap]
rs1170389	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs1170390	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.94[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1170391	0.81[CHB][hapmap];0.83[JPT][hapmap]
rs1170393	0.81[CHB][hapmap];0.83[JPT][hapmap]
rs11717610	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11718741	0.83[JPT][hapmap]
rs12171307	0.87[AFR][1000 genomes]
rs12485283	0.94[JPT][hapmap]
rs12492656	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13087364	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13088180	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1375580	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1375591	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1449443	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1449446	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16857897	1.00[CEU][hapmap];0.92[CHB][hapmap];0.94[JPT][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs16857919	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1707469	0.81[CHB][hapmap];0.81[CHD][hapmap];0.83[JPT][hapmap]
rs1868541	0.81[CHB][hapmap];0.83[JPT][hapmap]
rs1982382	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2175668	0.84[GIH][hapmap];0.88[JPT][hapmap]
rs3762694	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3792340	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3792345	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3804663	1.00[CEU][hapmap];0.92[CHB][hapmap];0.93[JPT][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3804667	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4611785	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4681293	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4681301	0.83[JPT][hapmap]
rs56686359	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6440420	0.92[YRI][hapmap];0.89[AFR][1000 genomes]
rs6771106	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6771118	0.90[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.83[JPT][hapmap];0.88[LWK][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6775684	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6781300	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6783926	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6792464	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6794727	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7613150	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7628805	0.94[JPT][hapmap]
rs7639115	0.87[AFR][1000 genomes]
rs7642940	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9820945	1.00[ASW][hapmap];1.00[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];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9823126	0.83[EUR][1000 genomes]
rs9836725	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9869137	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9881772	0.87[LWK][hapmap];0.84[YRI][hapmap]

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	nsv525829	chr3:145614317-145863779	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv4046	chr3:145693249-145880189	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	nsv877613	chr3:145833232-145912055	Weak transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4681297	SLC9A9	cis	parietal	SCAN
rs4681297	PLOD2	cis	parietal	SCAN
rs4681297	HLTF	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:145782800-145843200	Weak transcription	Pancreas	Pancrea
2	chr3:145784600-145848800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr3:145790400-145843200	Weak transcription	Right Ventricle	heart
4	chr3:145798800-145839200	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr3:145810400-145849800	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr3:145810800-145851200	Weak transcription	Brain Hippocampus Middle	brain
7	chr3:145812200-145839200	Weak transcription	Rectal Smooth Muscle	rectum
8	chr3:145814200-145841000	Weak transcription	Lung	lung
9	chr3:145816400-145842000	Weak transcription	Colonic Mucosa	Colon
10	chr3:145819800-145841800	Weak transcription	Fetal Heart	heart
11	chr3:145819800-145849200	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr3:145821000-145849800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr3:145824600-145839600	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr3:145827000-145855200	Weak transcription	Aorta	Aorta
15	chr3:145827400-145840200	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr3:145827400-145842000	Weak transcription	Duodenum Mucosa	Duodenum
17	chr3:145831400-145848400	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr3:145832000-145870800	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr3:145832600-145848400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr3:145833600-145843200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr3:145834200-145851200	Weak transcription	HUES48 Cell Line	embryonic stem cell
22	chr3:145834400-145839000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr3:145834400-145839600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr3:145834400-145851400	Weak transcription	Primary hematopoietic stem cells	blood
25	chr3:145834600-145841200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
26	chr3:145834600-145852800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr3:145835200-145851200	Weak transcription	HUES64 Cell Line	embryonic stem cell
28	chr3:145835200-145852200	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr3:145835600-145843600	Weak transcription	NHEK	skin
30	chr3:145835600-145851200	Weak transcription	Fetal Kidney	kidney
31	chr3:145835800-145843200	Weak transcription	Small Intestine	intestine
32	chr3:145835800-145846000	Weak transcription	Fetal Intestine Small	intestine
33	chr3:145835800-145874000	Weak transcription	Psoas Muscle	Psoas
34	chr3:145836000-145852400	Weak transcription	Duodenum Smooth Muscle	Duodenum
35	chr3:145836200-145839000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr3:145836200-145840200	Weak transcription	HMEC	breast
37	chr3:145836200-145844200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr3:145836800-145839800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr3:145836800-145844000	Weak transcription	NHLF	lung
40	chr3:145837000-145841800	Weak transcription	Placenta	Placenta
41	chr3:145837000-145843200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr3:145837000-145843200	Weak transcription	Esophagus	oesophagus
43	chr3:145837000-145844200	Weak transcription	NHDF-Ad	bronchial
44	chr3:145837000-145848800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr3:145837000-145852400	Weak transcription	HUES6 Cell Line	embryonic stem cell
46	chr3:145837200-145839600	Weak transcription	Fetal Intestine Large	intestine
47	chr3:145837200-145839600	Weak transcription	Ovary	ovary
48	chr3:145837200-145839600	Weak transcription	HSMMtube	muscle
49	chr3:145837200-145840800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr3:145837200-145842200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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