Variant report

Variant	rs10929178
Chromosome Location	chr2:234396566-234396567
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:234393460..234398388-chr2:234612624..234620814,16	MCF-7	breast:
2	chr2:234388753..234400184-chr2:234596527..234603213,35	MCF-7	breast:
3	chr2:234394199..234396835-chr2:234450285..234452802,2	MCF-7	breast:
4	chr2:234386983..234399433-chr2:234613282..234621553,23	MCF-7	breast:
5	chr2:234393753..234400835-chr2:234472864..234476478,8	MCF-7	breast:
6	chr2:234389632..234392009-chr2:234393676..234396865,6	MCF-7	breast:
7	chr2:234393680..234401613-chr2:234597738..234605139,18	MCF-7	breast:
8	chr2:234395375..234398231-chr2:234399551..234402111,5	MCF-7	breast:
9	chr2:234386214..234389809-chr2:234395089..234397205,3	MCF-7	breast:
10	chr2:234395319..234396920-chr2:234593778..234595799,2	MCF-7	breast:
11	chr2:234395630..234397717-chr2:234604680..234606573,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000224814	Chromatin interaction
ENSG00000085982	Chromatin interaction
ENSG00000167165	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs1046976	1.00[CHB][hapmap]
rs11675254	0.92[CEU][hapmap];1.00[CHB][hapmap]
rs11675858	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11676524	0.85[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.90[MEX][hapmap];0.88[MKK][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11686188	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.90[LWK][hapmap];0.90[MEX][hapmap];0.94[TSI][hapmap];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11694406	0.85[CEU][hapmap];1.00[CHB][hapmap]
rs2228939	0.82[AMR][1000 genomes]
rs3754595	0.92[CEU][hapmap];1.00[CHB][hapmap]
rs3796090	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes]
rs3796092	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3820744	0.92[CEU][hapmap];1.00[CHB][hapmap]
rs3828307	1.00[CHB][hapmap]
rs4047189	0.85[CEU][hapmap];0.83[CHD][hapmap];0.95[GIH][hapmap];0.89[JPT][hapmap];0.90[MEX][hapmap];0.92[MKK][hapmap];0.94[TSI][hapmap];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6704644	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.94[TSI][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6746234	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.87[LWK][hapmap];0.90[MEX][hapmap];0.98[MKK][hapmap];0.94[TSI][hapmap];0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6753242	0.92[CEU][hapmap];1.00[CHB][hapmap]
rs72980376	0.82[AMR][1000 genomes]
rs72980395	0.95[EUR][1000 genomes]
rs72980402	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72982309	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72982316	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72982325	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7587876	0.92[CEU][hapmap];1.00[CHB][hapmap]
rs7598771	0.85[CEU][hapmap];1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529419	chr2:234229606-234670426	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
2	nsv1000870	chr2:234333083-234410768	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv876013	chr2:234338227-234579915	Weak transcription Active TSS Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
4	nsv3214	chr2:234384436-234416949	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
5	nsv428072	chr2:234393609-234624769	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10929178	ECEL1P2	cis	parietal	SCAN

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:234343000-234402200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr2:234364000-234411200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr2:234373000-234409800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr2:234373800-234404400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr2:234375400-234411200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr2:234377800-234397200	Weak transcription	Small Intestine	intestine
7	chr2:234381600-234399600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr2:234383400-234400200	Strong transcription	Fetal Intestine Small	intestine
9	chr2:234384000-234412400	Weak transcription	Fetal Heart	heart
10	chr2:234384400-234398200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr2:234384400-234402200	Strong transcription	Rectal Mucosa Donor 29	rectum
12	chr2:234384400-234402600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr2:234384600-234408400	Strong transcription	Duodenum Mucosa	Duodenum
14	chr2:234386000-234397600	Weak transcription	Brain Germinal Matrix	brain
15	chr2:234386600-234400800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr2:234386800-234407800	Strong transcription	Fetal Intestine Large	intestine
17	chr2:234387200-234396600	Weak transcription	Psoas Muscle	Psoas
18	chr2:234387400-234402800	Strong transcription	Adipose Nuclei	Adipose
19	chr2:234387400-234466000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
20	chr2:234388200-234402000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr2:234388400-234401800	Strong transcription	Brain Inferior Temporal Lobe	brain
22	chr2:234388600-234396600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
23	chr2:234389800-234396800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr2:234389800-234398200	Strong transcription	Primary T helper cells fromperipheralblood	blood
25	chr2:234390200-234402800	Strong transcription	Rectal Mucosa Donor 31	rectum
26	chr2:234390800-234441000	Weak transcription	Fetal Brain Male	brain
27	chr2:234391200-234404400	Strong transcription	Fetal Stomach	stomach
28	chr2:234391400-234402600	Strong transcription	Skeletal Muscle Male	skeletal muscle
29	chr2:234391600-234397200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr2:234391600-234412000	Strong transcription	Skeletal Muscle Female	skeletal muscle
31	chr2:234391800-234398000	Strong transcription	Brain Anterior Caudate	brain
32	chr2:234392000-234411600	Weak transcription	Fetal Brain Female	brain
33	chr2:234392200-234402400	Strong transcription	Duodenum Smooth Muscle	Duodenum
34	chr2:234392400-234399400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
35	chr2:234392400-234403000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr2:234392800-234397000	Weak transcription	Thymus	Thymus
37	chr2:234392800-234398200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr2:234392800-234406400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
39	chr2:234393000-234400800	Weak transcription	GM12878-XiMat	blood
40	chr2:234393000-234402400	Weak transcription	HUES64 Cell Line	embryonic stem cell
41	chr2:234393600-234401000	Weak transcription	Pancreatic Islets	Pancreatic Islet
42	chr2:234393800-234403200	Strong transcription	Primary T cells from cord blood	blood
43	chr2:234394000-234396600	Weak transcription	Cortex derived primary cultured neurospheres	brain
44	chr2:234394000-234403200	Weak transcription	HUES6 Cell Line	embryonic stem cell
45	chr2:234394200-234402600	Strong transcription	Sigmoid Colon	Sigmoid Colon
46	chr2:234394400-234397400	Genic enhancers	Placenta	Placenta
47	chr2:234394400-234398400	Enhancers	Hela-S3	cervix
48	chr2:234394400-234399200	Weak transcription	Primary T helper cells PMA-I stimulated	--
49	chr2:234394400-234399600	Genic enhancers	NHEK	skin
50	chr2:234394400-234401000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood

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