Variant report

Variant	rs6433770
Chromosome Location	chr2:180117966-180117967
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	chr2:180116382..180118315-chr2:180123410..180126262,2	MCF-7	breast:
2	chr2:180114644..180119395-chr2:180127594..180130471,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000187231	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10164707	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs10177122	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10177402	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10181291	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10181464	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10182477	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10185803	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10194420	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10194534	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10204985	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10209183	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10209887	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10439300	0.87[AFR][1000 genomes]
rs10930859	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12105846	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12617002	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12621023	0.90[EUR][1000 genomes]
rs12621115	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12622075	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12623243	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12693179	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12693181	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12693183	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12987285	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs13020645	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs13382185	0.83[EUR][1000 genomes]
rs13384403	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13392996	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs13396340	0.83[EUR][1000 genomes]
rs13414296	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13417919	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2007593	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28838656	0.83[EUR][1000 genomes]
rs57098667	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs67043078	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6731614	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6759983	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7569887	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs7601366	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7608745	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs9288026	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];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	nsv949133	chr2:179711376-180124327	Flanking Active TSS ZNF genes & repeats Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
2	nsv1004693	chr2:179933683-180265288	Weak transcription Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
3	nsv834471	chr2:179974303-180123027	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
4	nsv834472	chr2:180091670-180220448	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6433770	SESTD1	cis	multi-tissue	Pritchard
rs6433770	SESTD1	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:180091800-180127200	Weak transcription	Fetal Lung	lung
2	chr2:180098600-180118600	Weak transcription	Pancreas	Pancrea
3	chr2:180102800-180127800	Weak transcription	Psoas Muscle	Psoas
4	chr2:180105600-180120000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr2:180110200-180124200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr2:180111200-180120400	Enhancers	Primary B cells from peripheral blood	blood
7	chr2:180112200-180120000	Weak transcription	Fetal Kidney	kidney
8	chr2:180112400-180126200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr2:180112600-180118400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr2:180112600-180125000	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr2:180112600-180126800	Weak transcription	Hela-S3	cervix
12	chr2:180115400-180127600	Weak transcription	NHLF	lung
13	chr2:180116000-180118000	Enhancers	Colon Smooth Muscle	Colon
14	chr2:180116200-180118200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr2:180116200-180118400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr2:180116200-180118600	Flanking Active TSS	Primary B cells from cord blood	blood
17	chr2:180116200-180124400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr2:180116400-180118600	Enhancers	Monocytes-CD14+_RO01746	blood
19	chr2:180116600-180118200	Enhancers	Osteobl	bone
20	chr2:180116800-180118000	Enhancers	Primary hematopoietic stem cells	blood
21	chr2:180116800-180118600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr2:180116800-180118800	Enhancers	Adipose Nuclei	Adipose
23	chr2:180116800-180124400	Enhancers	HepG2	liver
24	chr2:180117000-180118000	Flanking Active TSS	GM12878-XiMat	blood
25	chr2:180117000-180118200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr2:180117200-180118000	Enhancers	iPS-18 Cell Line	embryonic stem cell
27	chr2:180117200-180118200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr2:180117400-180118200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr2:180117400-180126200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr2:180117600-180118000	Enhancers	Brain Angular Gyrus	brain
31	chr2:180117600-180118200	Enhancers	Brain Cingulate Gyrus	brain
32	chr2:180117600-180118200	Enhancers	Brain Hippocampus Middle	brain
33	chr2:180117600-180118200	Enhancers	Rectal Smooth Muscle	rectum
34	chr2:180117600-180119000	Weak transcription	H9 Cell Line	embryonic stem cell
35	chr2:180117600-180119200	Weak transcription	Brain Anterior Caudate	brain
36	chr2:180117800-180118200	Enhancers	Duodenum Smooth Muscle	Duodenum
37	chr2:180117800-180119200	Weak transcription	HUES48 Cell Line	embryonic stem cell
38	chr2:180117800-180119200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
39	chr2:180117800-180119200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
40	chr2:180117800-180124400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr2:180117800-180126400	Weak transcription	Small Intestine	intestine

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