Variant report

Variant	rs3769166
Chromosome Location	chr2:174058828-174058829
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	chr2:174055885..174057518-chr2:174057984..174059551,2	MCF-7	breast:
2	chr2:173939636..173941413-chr2:174058307..174059908,2	K562	blood:

Variant related genes	Relation type
ENSG00000091436	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs11901996	0.85[CEU][hapmap];0.85[GIH][hapmap];0.80[TSI][hapmap]
rs12996371	0.80[JPT][hapmap]
rs16861266	0.84[CHD][hapmap]
rs16861279	0.84[JPT][hapmap]
rs16861295	0.90[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs16861304	0.88[ASW][hapmap];0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16861323	1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs2053964	0.81[JPT][hapmap]
rs2119123	0.85[JPT][hapmap]
rs2119124	0.94[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2289395	1.00[CHB][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs3769155	1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.86[LWK][hapmap];0.89[MEX][hapmap];0.87[MKK][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs3769164	0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs3769175	0.85[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs3769176	0.93[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.91[TSI][hapmap];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3769179	0.88[ASW][hapmap];0.85[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3769183	0.95[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs4632313	0.81[CHD][hapmap];0.82[JPT][hapmap]
rs58407376	0.96[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59935415	0.99[ASN][1000 genomes]
rs61183795	0.81[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs6433398	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs6717067	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs6725795	0.84[CEU][hapmap]
rs6753354	0.94[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.93[TSI][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73971702	0.99[ASN][1000 genomes]
rs7566222	0.94[CHB][hapmap];0.94[JPT][hapmap];0.99[ASN][1000 genomes]
rs7571788	0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1011724	chr2:173916482-174231908	Enhancers Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
2	nsv834460	chr2:173919464-174085288	Strong transcription Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3769166	HOXD4	cis	parietal	SCAN

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:174026000-174069000	Weak transcription	Primary B cells from cord blood	blood
2	chr2:174026600-174083200	Weak transcription	Esophagus	oesophagus
3	chr2:174046400-174075800	Weak transcription	Duodenum Mucosa	Duodenum
4	chr2:174047000-174062800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr2:174047600-174060800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr2:174047600-174062800	Weak transcription	GM12878-XiMat	blood
7	chr2:174047800-174065800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr2:174048600-174095200	Weak transcription	Thymus	Thymus
9	chr2:174049000-174070600	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr2:174049200-174070200	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr2:174049200-174083200	Weak transcription	Small Intestine	intestine
12	chr2:174049400-174060600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr2:174049400-174060800	Weak transcription	Lung	lung
14	chr2:174049400-174060800	Weak transcription	Right Ventricle	heart
15	chr2:174049400-174078200	Weak transcription	HUVEC	blood vessel
16	chr2:174049600-174062800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr2:174049600-174074400	Weak transcription	Fetal Stomach	stomach
18	chr2:174049600-174079800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr2:174049800-174062600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr2:174050200-174062800	Weak transcription	HepG2	liver
21	chr2:174051600-174065200	Strong transcription	Monocytes-CD14+_RO01746	blood
22	chr2:174052000-174059600	Weak transcription	Aorta	Aorta
23	chr2:174052000-174063000	Weak transcription	Placenta	Placenta
24	chr2:174052800-174063200	Weak transcription	Primary B cells from peripheral blood	blood
25	chr2:174053000-174065400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr2:174053400-174060800	Weak transcription	Fetal Intestine Small	intestine
27	chr2:174053400-174062800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr2:174053400-174072000	Weak transcription	Right Atrium	heart
29	chr2:174053400-174075600	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr2:174053400-174078400	Weak transcription	Gastric	stomach
31	chr2:174053400-174082000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr2:174053400-174089800	Weak transcription	Pancreas	Pancrea
33	chr2:174053600-174062800	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr2:174054600-174059000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
35	chr2:174054600-174061800	Enhancers	iPS-18 Cell Line	embryonic stem cell
36	chr2:174054800-174062800	Weak transcription	Fetal Muscle Trunk	muscle
37	chr2:174055000-174065000	Weak transcription	Primary T cells from cord blood	blood
38	chr2:174055200-174059600	Weak transcription	Psoas Muscle	Psoas
39	chr2:174055400-174064800	Weak transcription	Rectal Mucosa Donor 29	rectum
40	chr2:174055800-174060600	Enhancers	Rectal Smooth Muscle	rectum
41	chr2:174055800-174061800	Enhancers	HUES48 Cell Line	embryonic stem cell
42	chr2:174056000-174059800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
43	chr2:174056000-174060600	Enhancers	HUES6 Cell Line	embryonic stem cell
44	chr2:174056000-174061400	Enhancers	H1 Cell Line	embryonic stem cell
45	chr2:174056000-174061800	Enhancers	iPS-15b Cell Line	embryonic stem cell
46	chr2:174056400-174059000	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr2:174056400-174059600	Enhancers	Fetal Heart	heart
48	chr2:174056400-174060600	Enhancers	Stomach Smooth Muscle	stomach
49	chr2:174056400-174062800	Weak transcription	K562	blood
50	chr2:174056400-174063000	Weak transcription	Fetal Thymus	thymus

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