Variant report

Variant	rs2861422
Chromosome Location	chr3:141724644-141724645
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	JUN	chr3:141724513-141724664	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:141724450..141726280-chr3:141745104..141746996,2	K562	blood:

Variant related genes	Relation type
TFDP2	TF binding region

Extended variants
information (count: 51 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10935453	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.96[ASN][1000 genomes]
rs11569198	0.83[CHB][hapmap]
rs11706480	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11714792	0.80[ASN][1000 genomes]
rs12496412	0.98[ASN][1000 genomes]
rs13065446	0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs1355438	0.94[CEU][hapmap];0.94[CHB][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.91[TSI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1397764	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1511299	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1543064	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs1704985	0.87[EUR][1000 genomes]
rs1705607	0.87[EUR][1000 genomes]
rs1705614	0.85[EUR][1000 genomes]
rs1705624	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2063453	0.83[CHB][hapmap]
rs2063454	0.83[CHB][hapmap]
rs2271386	0.83[CHB][hapmap]
rs2862125	0.95[ASN][1000 genomes]
rs34186890	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34392664	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs347685	0.87[EUR][1000 genomes]
rs347686	0.87[EUR][1000 genomes]
rs347692	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3817176	0.83[CHB][hapmap]
rs4683658	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62283130	0.82[EUR][1000 genomes]
rs6440057	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6440060	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6773343	0.94[CEU][hapmap];0.88[JPT][hapmap];0.87[MEX][hapmap];0.88[TSI][hapmap];0.82[EUR][1000 genomes]
rs6778085	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs6781340	0.96[ASN][1000 genomes]
rs6791514	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6794342	0.85[ASN][1000 genomes]
rs6795301	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs72990266	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7619506	0.82[CHB][hapmap]
rs7630893	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7644155	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7644383	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9289641	0.82[JPT][hapmap]
rs963396	0.83[CHB][hapmap]
rs9848817	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs9857917	0.84[EUR][1000 genomes]
rs9865413	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9865777	0.82[JPT][hapmap]
rs9877536	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9877817	0.94[CEU][hapmap];0.84[CHB][hapmap];0.80[CHD][hapmap];0.89[JPT][hapmap];0.88[MEX][hapmap];0.92[TSI][hapmap];0.85[EUR][1000 genomes]
rs9942075	0.94[CHB][hapmap];0.82[CHD][hapmap];0.88[JPT][hapmap];0.82[MEX][hapmap];0.86[ASN][1000 genomes]

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	nsv949709	chr3:141295050-142178144	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	nsv1013352	chr3:141541105-141870293	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	nsv1002446	chr3:141719169-142070290	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2861422	CHST2	cis	cerebellum	SCAN
rs2861422	XRN1	cis	parietal	SCAN

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:141629000-141739200	Weak transcription	Psoas Muscle	Psoas
2	chr3:141671800-141735600	Weak transcription	Aorta	Aorta
3	chr3:141677800-141739000	Weak transcription	Left Ventricle	heart
4	chr3:141678800-141745600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
5	chr3:141680000-141731200	Weak transcription	Fetal Brain Female	brain
6	chr3:141682800-141739000	Weak transcription	Pancreas	Pancrea
7	chr3:141682800-141745800	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr3:141682800-141746200	Weak transcription	Primary B cells from peripheral blood	blood
9	chr3:141683800-141746600	Weak transcription	Lung	lung
10	chr3:141688800-141729000	Strong transcription	Fetal Thymus	thymus
11	chr3:141697400-141727200	Weak transcription	Primary neutrophils fromperipheralblood	blood
12	chr3:141697600-141725800	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr3:141698600-141738800	Weak transcription	HSMM	muscle
14	chr3:141704200-141725400	Weak transcription	Spleen	Spleen
15	chr3:141706400-141746200	Weak transcription	Fetal Lung	lung
16	chr3:141707200-141734400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr3:141708400-141731200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr3:141708600-141728400	Weak transcription	Liver	Liver
19	chr3:141708600-141745200	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr3:141711800-141732400	Weak transcription	Stomach Smooth Muscle	stomach
21	chr3:141716000-141732400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr3:141716000-141738600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr3:141716000-141745600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr3:141719600-141738600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr3:141719600-141738600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr3:141719600-141739000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr3:141719800-141728600	Strong transcription	Dnd41	blood
28	chr3:141720200-141725800	Weak transcription	Fetal Muscle Trunk	muscle
29	chr3:141720200-141738000	Weak transcription	Fetal Intestine Large	intestine
30	chr3:141720200-141746600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr3:141720400-141732400	Weak transcription	Fetal Stomach	stomach
32	chr3:141720400-141737400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr3:141720400-141742600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr3:141720600-141730000	Weak transcription	Primary T cells from cord blood	blood
35	chr3:141721200-141725400	Weak transcription	Fetal Intestine Small	intestine
36	chr3:141721600-141739000	Weak transcription	Fetal Muscle Leg	muscle
37	chr3:141722600-141735600	Weak transcription	Thymus	Thymus
38	chr3:141722600-141745400	Weak transcription	Cortex derived primary cultured neurospheres	brain
39	chr3:141723000-141727000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr3:141723400-141726800	Weak transcription	K562	blood
41	chr3:141723400-141727200	Weak transcription	Colon Smooth Muscle	Colon
42	chr3:141723400-141731600	Weak transcription	Rectal Smooth Muscle	rectum
43	chr3:141723400-141745400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr3:141723400-141745400	Weak transcription	Fetal Kidney	kidney
45	chr3:141723600-141738400	Weak transcription	Primary B cells from cord blood	blood
46	chr3:141724200-141730600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr3:141724200-141731200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
48	chr3:141724400-141733000	Weak transcription	Primary hematopoietic stem cells	blood
49	chr3:141724400-141738600	Weak transcription	HUES64 Cell Line	embryonic stem cell
50	chr3:141724400-141741200	Weak transcription	iPS-18 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links