Variant report

Variant	rs12723898
Chromosome Location	chr1:151552672-151552673
allele	A/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:20)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:20 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:151549985..151552778-chr1:151557616..151559684,2	MCF-7	breast:
2	1:151496437-151509688..1:151546427-151553405	Hela-S3	cervix:
3	1:151270864-151283078..1:151546427-151553405	K562	blood:
4	chr1:151547358..151549969-chr1:151551403..151554621,3	MCF-7	breast:
5	chr1:151508189..151514847-chr1:151547303..151553587,9	MCF-7	breast:
6	1:151516085-151535167..1:151546427-151553405	GM12878	blood:
7	1:151512437-151516085..1:151546427-151553405	Hela-S3	cervix:
8	1:151254384-151268403..1:151546427-151553405	GM12878	blood:
9	chr1:151510996..151514435-chr1:151551077..151556153,9	MCF-7	breast:
10	1:151426875-151427826..1:151546427-151553405	Hela-S3	cervix:
11	1:151219411-151234038..1:151546427-151553405	GM12878	blood:
12	1:151203965-151215310..1:151546427-151553405	GM12878	blood:
13	chr1:151547303..151551460-chr1:151552210..151554912,4	K562	blood:
14	1:151427826-151434310..1:151546427-151553405	Hela-S3	cervix:
15	chr1:151519527..151521373-chr1:151550797..151553176,2	MCF-7	breast:
16	chr1:151550211..151552157-chr1:151552278..151554643,2	MCF-7	breast:
17	1:151411623-151426875..1:151546427-151553405	GM12878	blood:
18	1:151368336-151375897..1:151546427-151553405	GM12878	blood:
19	1:151309061-151322694..1:151546427-151553405	Hela-S3	cervix:
20	1:151546427-151553405..1:151618750-151636526	GM12878	blood:

No data

Variant related genes	Relation type
ENSG00000143398	Chromatin interaction
ENSG00000232536	Chromatin interaction
ENSG00000207606	Chromatin interaction
ENSG00000237976	Chromatin interaction
ENSG00000143375	Chromatin interaction
ENSG00000143376	Chromatin interaction
ENSG00000223861	Chromatin interaction
ENSG00000143393	Chromatin interaction
ENSG00000232671	Chromatin interaction
ENSG00000265753	Chromatin interaction
ENSG00000252840	Chromatin interaction
ENSG00000159377	Chromatin interaction
ENSG00000143390	Chromatin interaction
ENSG00000159352	Chromatin interaction
ENSG00000143367	Chromatin interaction
ENSG00000143442	Chromatin interaction
ENSG00000224645	Chromatin interaction
ENSG00000143373	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10218788	0.95[EUR][1000 genomes]
rs10494267	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11807809	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12090862	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12564097	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12734011	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12734511	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12747024	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12747990	0.91[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12751350	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];0.96[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1539490	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1891592	1.00[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.93[LWK][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1935886	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34180474	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34690266	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3748608	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3748609	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3748610	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4970919	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6587605	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6675022	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6679183	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6691958	0.95[CEU][hapmap];0.81[CHD][hapmap];0.89[GIH][hapmap];0.83[JPT][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes]
rs6698282	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6704177	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7554707	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];0.92[MEX][hapmap];0.94[TSI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[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	nsv916272	chr1:150961809-151557253	Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	219 gene(s)	inside rSNPs	diseases
2	nsv997511	chr1:151491765-151595902	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12723898	TUFT1	cis	parietal	SCAN
rs12723898	FLG2	cis	cerebellum	SCAN

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151514400-151556800	Weak transcription	Fetal Brain Male	brain
2	chr1:151521800-151559000	Weak transcription	Small Intestine	intestine
3	chr1:151533000-151557200	Weak transcription	Primary T helper cells fromperipheralblood	blood
4	chr1:151533800-151561600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr1:151535800-151561800	Weak transcription	Brain Substantia Nigra	brain
6	chr1:151537000-151556800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr1:151537400-151556000	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr1:151537400-151558400	Weak transcription	Fetal Kidney	kidney
9	chr1:151538000-151557400	Weak transcription	Brain Hippocampus Middle	brain
10	chr1:151539000-151556400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr1:151539000-151557000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr1:151539600-151555400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr1:151541000-151553200	Strong transcription	Fetal Muscle Leg	muscle
14	chr1:151541200-151557000	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr1:151541400-151556400	Strong transcription	Fetal Stomach	stomach
16	chr1:151542000-151557000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr1:151542600-151557400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr1:151542800-151556600	Strong transcription	Fetal Intestine Small	intestine
19	chr1:151542800-151556600	Strong transcription	Rectal Mucosa Donor 29	rectum
20	chr1:151543800-151556400	Strong transcription	Fetal Intestine Large	intestine
21	chr1:151545200-151555000	Strong transcription	Sigmoid Colon	Sigmoid Colon
22	chr1:151545200-151556600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr1:151545800-151553000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr1:151546400-151555200	Strong transcription	Rectal Mucosa Donor 31	rectum
25	chr1:151546600-151552800	Strong transcription	Colon Smooth Muscle	Colon
26	chr1:151547400-151553200	Weak transcription	Brain Angular Gyrus	brain
27	chr1:151547400-151556000	Weak transcription	Spleen	Spleen
28	chr1:151547600-151556200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr1:151547600-151556200	Weak transcription	HUVEC	blood vessel
30	chr1:151548000-151555000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr1:151548000-151556200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
32	chr1:151548000-151556800	Weak transcription	Cortex derived primary cultured neurospheres	brain
33	chr1:151548000-151557200	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr1:151548400-151557400	Weak transcription	Brain Cingulate Gyrus	brain
35	chr1:151548800-151557200	Strong transcription	Brain Germinal Matrix	brain
36	chr1:151548800-151558200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr1:151549000-151556200	Weak transcription	Skeletal Muscle Female	skeletal muscle
38	chr1:151549400-151552800	Genic enhancers	NHEK	skin
39	chr1:151550000-151553400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
40	chr1:151550000-151554800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
41	chr1:151550000-151556400	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr1:151550200-151553600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
43	chr1:151550200-151555000	Genic enhancers	Placenta	Placenta
44	chr1:151550200-151556600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
45	chr1:151550400-151559800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr1:151550600-151554400	Strong transcription	Fetal Brain Female	brain
47	chr1:151550800-151554800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr1:151550800-151554800	Strong transcription	Aorta	Aorta
49	chr1:151550800-151555000	Strong transcription	HUES64 Cell Line	embryonic stem cell
50	chr1:151550800-151555000	Strong transcription	Breast Myoepithelial Primary Cells	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links