Variant report

Variant	rs16859371
Chromosome Location	chr2:172241568-172241569
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	chr2:172238421..172241638-chr2:172288610..172290527,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000123600	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs16859368	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16859373	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16859377	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16859380	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16859386	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16859390	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16859404	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16859405	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16859410	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17287497	0.83[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs1882378	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3731984	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3795996	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55711751	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55715902	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55716501	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs55974181	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56065525	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56239048	0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56273218	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56302833	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57165050	0.88[EUR][1000 genomes]
rs61021737	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61502503	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6759487	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[ASN][1000 genomes]
rs728651	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72882347	0.83[AFR][1000 genomes]
rs72882363	0.83[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs73021048	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73976175	0.92[EUR][1000 genomes]
rs9646734	1.00[CHB][hapmap];1.00[JPT][hapmap];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	esv3382346	chr2:172062677-172363892	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:172211000-172242600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr2:172222200-172289600	Weak transcription	Gastric	stomach
3	chr2:172223000-172242000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr2:172229400-172246800	Weak transcription	NH-A	brain
5	chr2:172231400-172248000	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr2:172231800-172243200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr2:172231800-172248200	Weak transcription	Esophagus	oesophagus
8	chr2:172232000-172253200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr2:172232200-172242000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr2:172232600-172242000	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr2:172232800-172241800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr2:172235400-172244600	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr2:172235600-172243400	Weak transcription	Primary hematopoietic stem cells	blood
14	chr2:172237800-172244600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr2:172237800-172254400	Weak transcription	Primary T helper cells fromperipheralblood	blood
16	chr2:172238000-172272400	Weak transcription	Fetal Intestine Large	intestine
17	chr2:172238200-172243400	Weak transcription	Primary B cells from cord blood	blood
18	chr2:172238600-172247200	Weak transcription	NHEK	skin
19	chr2:172238800-172246800	Weak transcription	HMEC	breast
20	chr2:172238800-172272400	Weak transcription	Primary T cells from cord blood	blood
21	chr2:172239000-172248000	Weak transcription	HepG2	liver
22	chr2:172239000-172250000	Weak transcription	Fetal Stomach	stomach
23	chr2:172239200-172242000	Weak transcription	HUES48 Cell Line	embryonic stem cell
24	chr2:172239200-172242000	Weak transcription	Fetal Intestine Small	intestine
25	chr2:172239200-172250400	Weak transcription	Fetal Heart	heart
26	chr2:172239200-172250600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr2:172239200-172257400	Weak transcription	K562	blood
28	chr2:172239400-172242000	Weak transcription	HUES64 Cell Line	embryonic stem cell
29	chr2:172239600-172243400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
30	chr2:172239600-172247600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
31	chr2:172240000-172243000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr2:172240000-172248000	Weak transcription	Colon Smooth Muscle	Colon
33	chr2:172240200-172247800	Weak transcription	NHLF	lung
34	chr2:172240600-172243200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr2:172240600-172244200	Weak transcription	GM12878-XiMat	blood
36	chr2:172240600-172244400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr2:172240600-172247000	Weak transcription	HSMMtube	muscle
38	chr2:172240600-172251000	Weak transcription	Rectal Mucosa Donor 31	rectum
39	chr2:172241000-172242600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr2:172241000-172243200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr2:172241400-172247400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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