Variant report

Variant	rs2917779
Chromosome Location	chr2:55472868-55472869
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:55471561..55473794-chr2:55479566..55481301,2	MCF-7	breast:

Extended variants
information (count: 46 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10193886	0.89[YRI][hapmap]
rs10200120	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10200424	0.89[YRI][hapmap]
rs1056445	0.82[ASW][hapmap];0.94[CEU][hapmap];0.86[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11357	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12052613	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12988617	0.85[ASN][1000 genomes]
rs13420684	0.82[YRI][hapmap]
rs1437393	0.89[YRI][hapmap]
rs17852670	0.81[ASN][1000 genomes]
rs2118284	0.82[YRI][hapmap]
rs2576708	0.81[AFR][1000 genomes]
rs2576711	0.88[ASW][hapmap];0.91[CHB][hapmap];0.87[CHD][hapmap];0.91[JPT][hapmap];0.81[MKK][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs2576712	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2576719	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2576721	0.94[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs2589080	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2589092	0.82[ASW][hapmap];0.94[CEU][hapmap];0.90[CHB][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2589093	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2589094	0.94[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.96[TSI][hapmap];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2589096	0.82[ASW][hapmap];0.90[CHB][hapmap];0.87[CHD][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs2589100	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2864819	0.92[ASN][1000 genomes]
rs2864826	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2920967	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34348115	0.95[CHB][hapmap];0.87[CHD][hapmap];0.85[ASN][1000 genomes]
rs34511570	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4435493	0.85[CHB][hapmap];0.90[CHD][hapmap];0.82[ASN][1000 genomes]
rs55997390	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56039135	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs6545477	0.86[YRI][hapmap]
rs6545480	0.94[CEU][hapmap];0.85[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs6706815	0.82[ASN][1000 genomes]
rs6711753	0.86[YRI][hapmap]
rs6727118	0.89[YRI][hapmap]
rs6727131	0.86[YRI][hapmap]
rs6737227	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs6747364	0.86[YRI][hapmap]
rs6755515	0.87[ASN][1000 genomes]
rs72799507	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7580936	0.83[EUR][1000 genomes]
rs7597293	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs934709	0.87[CHD][hapmap]
rs9677948	0.86[YRI][hapmap]

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	nsv522016	chr2:55404794-55560298	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats 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
2	esv3348896	chr2:55429540-55498552	Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2917779	CLHC1	cis	Artery Tibial	GTEx
rs2917779	CLHC1	cis	Adipose Subcutaneous	GTEx
rs2917779	LOC388720///RPS27A	Cis_1M	lymphoblastoid	RTeQTL
rs2917779	FLJ31438	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55461400-55477600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:55461600-55477000	Strong transcription	Fetal Muscle Leg	muscle
3	chr2:55461600-55481600	Strong transcription	Fetal Thymus	thymus
4	chr2:55461600-55495400	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr2:55461600-55495400	Weak transcription	Stomach Mucosa	stomach
6	chr2:55461800-55474400	Strong transcription	Primary T cells fromperipheralblood	blood
7	chr2:55461800-55493400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr2:55461800-55495000	Weak transcription	Fetal Brain Male	brain
9	chr2:55462000-55493200	Strong transcription	Duodenum Mucosa	Duodenum
10	chr2:55462200-55473200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr2:55462200-55490200	Weak transcription	Small Intestine	intestine
12	chr2:55462400-55476800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr2:55462400-55476800	Strong transcription	Rectal Mucosa Donor 29	rectum
14	chr2:55462600-55485800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr2:55463000-55477600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr2:55463000-55480200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
17	chr2:55463000-55481000	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr2:55463000-55495400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr2:55463200-55481000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr2:55463400-55474200	Weak transcription	Aorta	Aorta
21	chr2:55463400-55475800	Weak transcription	Spleen	Spleen
22	chr2:55463400-55488200	Weak transcription	Pancreas	Pancrea
23	chr2:55463600-55474800	Weak transcription	Thymus	Thymus
24	chr2:55463600-55483800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr2:55463800-55475400	Weak transcription	Esophagus	oesophagus
26	chr2:55463800-55479600	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr2:55463800-55486200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
28	chr2:55463800-55490400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
29	chr2:55463800-55494800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr2:55463800-55495600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr2:55464000-55476200	Weak transcription	Fetal Kidney	kidney
32	chr2:55464200-55473600	Weak transcription	Brain Cingulate Gyrus	brain
33	chr2:55464400-55476200	Weak transcription	Brain Angular Gyrus	brain
34	chr2:55464400-55479600	Weak transcription	NHLF	lung
35	chr2:55464600-55475600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr2:55464600-55476200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr2:55464600-55476200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr2:55464600-55479400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
39	chr2:55464600-55495800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
40	chr2:55465400-55490600	Weak transcription	Brain Germinal Matrix	brain
41	chr2:55465600-55473200	Weak transcription	HUVEC	blood vessel
42	chr2:55465600-55486000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
43	chr2:55465600-55494400	Strong transcription	HUES64 Cell Line	embryonic stem cell
44	chr2:55465800-55476400	Strong transcription	Primary B cells from peripheral blood	blood
45	chr2:55465800-55477600	Strong transcription	HUES48 Cell Line	embryonic stem cell
46	chr2:55466000-55493200	Strong transcription	Rectal Mucosa Donor 31	rectum
47	chr2:55466200-55476600	Strong transcription	Fetal Lung	lung
48	chr2:55466600-55475000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
49	chr2:55467400-55474600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr2:55468000-55477600	Strong transcription	Primary hematopoietic stem cells short term culture	blood

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