Variant report

Variant	rs2402945
Chromosome Location	chr7:128956256-128956257
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	chr7:128946459..128948231-chr7:128955623..128958607,2	MCF-7	breast:
2	chr7:128955714..128958015-chr7:129010766..129013650,2	K562	blood:

Extended variants
information (count: 107 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:103)

rs_ID	r²[population]
rs1000676	0.86[JPT][hapmap]
rs10248810	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs10954226	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10954230	0.86[JPT][hapmap]
rs11763056	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11763325	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11769045	0.96[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11979476	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12111832	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12112374	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12216567	0.91[ASN][1000 genomes]
rs12534372	0.86[JPT][hapmap]
rs12540568	0.86[JPT][hapmap]
rs12667132	0.86[JPT][hapmap]
rs12668958	0.93[CHD][hapmap];0.90[JPT][hapmap]
rs13226649	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13235668	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13235749	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1473236	0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1526900	0.95[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs1559486	0.95[CEU][hapmap];0.80[CHB][hapmap];0.82[CHD][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.86[EUR][1000 genomes]
rs17168512	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1880854	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2012919	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2056694	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2103232	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2141075	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2303303	0.84[EUR][1000 genomes]
rs2402944	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2566885	0.97[ASN][1000 genomes]
rs2566886	0.97[ASN][1000 genomes]
rs2694572	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.96[ASN][1000 genomes]
rs2694574	0.85[CEU][hapmap];0.89[JPT][hapmap]
rs2718083	0.86[CEU][hapmap];0.86[JPT][hapmap]
rs2718084	0.95[CEU][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap];0.97[TSI][hapmap];0.89[EUR][1000 genomes]
rs2718086	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2718089	0.98[ASN][1000 genomes]
rs2718093	0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2718096	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28636722	0.84[EUR][1000 genomes]
rs4440569	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4728163	0.86[JPT][hapmap]
rs4728164	0.86[JPT][hapmap]
rs4731569	0.82[ASN][1000 genomes]
rs4731572	0.86[JPT][hapmap]
rs4731575	0.85[JPT][hapmap]
rs55638303	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs56026912	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57263220	0.82[EUR][1000 genomes]
rs59659852	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs598412	0.82[MEX][hapmap]
rs60275163	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs644723	0.81[CEU][hapmap]
rs6467233	0.89[ASW][hapmap];0.95[CEU][hapmap];0.86[GIH][hapmap];0.86[JPT][hapmap];0.97[LWK][hapmap];0.95[MEX][hapmap];0.98[MKK][hapmap];0.92[TSI][hapmap];0.94[YRI][hapmap];0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6467235	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6467237	1.00[ASN][1000 genomes]
rs6467240	0.96[ASN][1000 genomes]
rs6467241	0.97[ASN][1000 genomes]
rs6467242	0.94[ASN][1000 genomes]
rs6467243	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs66538149	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs66864889	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66970518	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs67520056	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs67820265	0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs67853067	0.87[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs67997229	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs68076553	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs68184415	0.96[ASN][1000 genomes]
rs68187585	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs691158	0.80[CEU][hapmap]
rs692697	0.85[MEX][hapmap]
rs6942756	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6946288	0.82[ASN][1000 genomes]
rs6946938	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6948252	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6949950	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6953598	0.82[EUR][1000 genomes]
rs6966595	0.91[CEU][hapmap];0.80[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.87[TSI][hapmap];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6967464	0.96[ASN][1000 genomes]
rs6971917	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6974155	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6980385	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];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73472312	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7778277	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7780886	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7782348	0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7788327	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.96[ASN][1000 genomes]
rs7789697	0.80[EUR][1000 genomes]
rs7792317	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7794622	0.96[ASN][1000 genomes]
rs7800983	0.83[ASN][1000 genomes]
rs7803052	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7806089	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs822038	0.91[CEU][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap]
rs822040	0.91[CEU][hapmap];0.80[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.87[TSI][hapmap]
rs891545	0.82[CEU][hapmap];0.86[GIH][hapmap];0.86[JPT][hapmap];0.85[TSI][hapmap]
rs963465	0.82[CEU][hapmap];0.86[JPT][hapmap]
rs9640854	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9641846	0.82[CEU][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap];0.85[TSI][hapmap]
rs9641849	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9649530	0.82[ASN][1000 genomes]
rs9649531	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv525482	chr7:128890812-129045191	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv516498	chr7:128901429-129072024	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	esv3331483	chr7:128918442-129082887	Strong transcription Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
4	nsv428508	chr7:128946738-129114691	Enhancers Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2402945	FAM40B	cis	parietal	SCAN

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:128915000-128962600	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr7:128929200-128963800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr7:128941800-128962600	Weak transcription	Fetal Stomach	stomach
4	chr7:128943800-128961800	Weak transcription	Fetal Intestine Small	intestine
5	chr7:128944200-128963200	Weak transcription	Primary B cells from cord blood	blood
6	chr7:128945000-128963600	Weak transcription	Primary hematopoietic stem cells	blood
7	chr7:128945600-128966200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr7:128946800-128963600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr7:128947000-128957400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr7:128948000-128966600	Weak transcription	Pancreas	Pancrea
11	chr7:128948200-128959400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
12	chr7:128948200-128963600	Weak transcription	Esophagus	oesophagus
13	chr7:128948200-128963800	Weak transcription	Ovary	ovary
14	chr7:128948400-128964200	Weak transcription	Liver	Liver
15	chr7:128948800-128963200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr7:128951000-128962200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr7:128951800-128962800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr7:128953200-128957600	Enhancers	Skeletal Muscle Female	skeletal muscle
19	chr7:128954200-128956400	Enhancers	Psoas Muscle	Psoas
20	chr7:128954200-128956600	Enhancers	Fetal Muscle Leg	muscle
21	chr7:128954200-128963400	Weak transcription	Primary T helper cells fromperipheralblood	blood
22	chr7:128954600-128956800	Enhancers	Breast Myoepithelial Primary Cells	Breast
23	chr7:128954600-128957400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr7:128954600-128957800	Enhancers	Brain Anterior Caudate	brain
25	chr7:128954600-128958000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr7:128954800-128956800	Enhancers	Brain Angular Gyrus	brain
27	chr7:128954800-128957400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
28	chr7:128954800-128957600	Enhancers	Cortex derived primary cultured neurospheres	brain
29	chr7:128955000-128956800	Enhancers	Fetal Heart	heart
30	chr7:128955400-128956400	Enhancers	NHEK	skin
31	chr7:128955400-128956600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr7:128955400-128956800	Enhancers	Brain Cingulate Gyrus	brain
33	chr7:128955400-128956800	Enhancers	HSMMtube	muscle
34	chr7:128955600-128956400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr7:128955600-128956400	Enhancers	HMEC	breast
36	chr7:128955800-128956800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr7:128955800-128956800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr7:128955800-128957600	Enhancers	Brain Substantia Nigra	brain
39	chr7:128956000-128956400	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr7:128956000-128956400	Enhancers	Stomach Smooth Muscle	stomach
41	chr7:128956000-128962600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr7:128956000-128965000	Weak transcription	Primary T cells from cord blood	blood
43	chr7:128956000-128977400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
44	chr7:128956200-128956600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr7:128956200-128956600	Enhancers	Skeletal Muscle Male	skeletal muscle
46	chr7:128956200-128957800	Enhancers	Brain Hippocampus Middle	brain
47	chr7:128956200-128971400	Weak transcription	Left Ventricle	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links