Variant report

Variant	rs16859370
Chromosome Location	chr2:172240163-172240164
allele	A/C
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:
2	chr2:172238653..172240742-chr2:172242701..172246260,3	K562	blood:

Variant related genes	Relation type
ENSG00000123600	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10490603	0.82[JPT][hapmap];0.86[ASN][1000 genomes]
rs11696032	1.00[ASN][1000 genomes]
rs16823212	1.00[CHB][hapmap]
rs17219416	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2017090	1.00[CHB][hapmap]
rs62183546	0.89[ASN][1000 genomes]
rs72880576	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72880595	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72882305	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72882311	1.00[ASN][1000 genomes]
rs72882329	1.00[ASN][1000 genomes]
rs72882335	1.00[ASN][1000 genomes]
rs72882366	0.96[ASN][1000 genomes]
rs72882388	0.89[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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs16859370	STAT3	trans	brain	seeQTL
rs16859370	ATF2	cis	cerebellum	SCAN
rs16859370	SCRN3	cis	parietal	SCAN

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	chr2:172222400-172240200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr2:172223000-172242000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr2:172229400-172246800	Weak transcription	NH-A	brain
6	chr2:172231400-172248000	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr2:172231800-172240800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr2:172231800-172243200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr2:172231800-172248200	Weak transcription	Esophagus	oesophagus
10	chr2:172232000-172253200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr2:172232200-172242000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr2:172232600-172242000	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr2:172232800-172241800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
14	chr2:172235400-172244600	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr2:172235600-172243400	Weak transcription	Primary hematopoietic stem cells	blood
16	chr2:172237800-172244600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr2:172237800-172254400	Weak transcription	Primary T helper cells fromperipheralblood	blood
18	chr2:172238000-172272400	Weak transcription	Fetal Intestine Large	intestine
19	chr2:172238200-172243400	Weak transcription	Primary B cells from cord blood	blood
20	chr2:172238600-172247200	Weak transcription	NHEK	skin
21	chr2:172238800-172246800	Weak transcription	HMEC	breast
22	chr2:172238800-172272400	Weak transcription	Primary T cells from cord blood	blood
23	chr2:172239000-172240200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr2:172239000-172241000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr2:172239000-172248000	Weak transcription	HepG2	liver
26	chr2:172239000-172250000	Weak transcription	Fetal Stomach	stomach
27	chr2:172239200-172242000	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr2:172239200-172242000	Weak transcription	Fetal Intestine Small	intestine
29	chr2:172239200-172250400	Weak transcription	Fetal Heart	heart
30	chr2:172239200-172250600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr2:172239200-172257400	Weak transcription	K562	blood
32	chr2:172239400-172242000	Weak transcription	HUES64 Cell Line	embryonic stem cell
33	chr2:172239600-172243400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
34	chr2:172239600-172247600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
35	chr2:172240000-172240200	Enhancers	NHLF	lung
36	chr2:172240000-172240600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr2:172240000-172240600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
38	chr2:172240000-172240600	ZNF genes & repeats	GM12878-XiMat	blood
39	chr2:172240000-172240800	Enhancers	Liver	Liver
40	chr2:172240000-172243000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr2:172240000-172248000	Weak transcription	Colon Smooth Muscle	Colon

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