Variant report

Variant	rs10157197
Chromosome Location	chr1:150250636-150250637
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:150248568..150250658-chr1:150336049..150337557,2	MCF-7	breast:
2	chr1:150249314..150251862-chr1:150292690..150295830,3	MCF-7	breast:
3	chr1:150248711..150251373-chr1:150294056..150296780,2	MCF-7	breast:
4	chr1:150247383..150251206-chr1:150256020..150261990,7	K562	blood:

Variant related genes	Relation type
ENSG00000117360	Chromatin interaction
ENSG00000163125	Chromatin interaction

Extended variants
information (count: 98 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:93)

rs_ID	r²[population]
rs10788873	0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs10888577	0.82[MKK][hapmap]
rs10888578	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.91[TSI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10888579	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1097066	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1097069	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1097071	0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs11205355	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11205359	0.88[EUR][1000 genomes]
rs11205370	0.80[AMR][1000 genomes]
rs11205371	0.80[AMR][1000 genomes]
rs11205373	0.96[CEU][hapmap]
rs11205382	0.96[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.84[YRI][hapmap]
rs11590406	0.87[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs11811885	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12093148	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12122277	0.81[MKK][hapmap]
rs1260373	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1260385	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1260391	0.80[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs1260398	0.88[EUR][1000 genomes]
rs1260401	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1260403	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1260404	0.86[EUR][1000 genomes]
rs1260407	0.96[CEU][hapmap];0.90[GIH][hapmap];0.89[TSI][hapmap];0.86[EUR][1000 genomes]
rs1260408	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1260409	0.86[EUR][1000 genomes]
rs1260424	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1260457	0.96[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];0.88[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs1262432	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12731296	0.95[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap]
rs12739706	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1313568	0.96[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1313569	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1313570	0.82[EUR][1000 genomes]
rs1566225	0.95[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap]
rs1694364	0.96[CEU][hapmap];0.84[EUR][1000 genomes]
rs1694379	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.88[GIH][hapmap];0.91[JPT][hapmap];0.92[LWK][hapmap];0.87[MEX][hapmap];0.92[MKK][hapmap];0.89[TSI][hapmap];0.84[YRI][hapmap];0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1694380	0.95[CEU][hapmap];0.87[EUR][1000 genomes]
rs1694381	0.86[EUR][1000 genomes]
rs1694386	0.83[ASN][1000 genomes]
rs1747927	0.86[EUR][1000 genomes]
rs1776265	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1776270	0.83[ASN][1000 genomes]
rs1776272	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1776273	0.96[CEU][hapmap];0.90[GIH][hapmap];0.89[TSI][hapmap];0.89[EUR][1000 genomes]
rs1776275	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1776276	0.86[EUR][1000 genomes]
rs1932934	0.96[CEU][hapmap];0.90[GIH][hapmap];0.86[TSI][hapmap]
rs2133129	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2147324	0.86[GIH][hapmap]
rs2264417	0.96[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2454285	0.86[EUR][1000 genomes]
rs2762860	0.84[EUR][1000 genomes]
rs2794680	0.84[AMR][1000 genomes]
rs3125808	0.85[EUR][1000 genomes]
rs3818978	0.87[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.90[YRI][hapmap];0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs471738	0.96[CEU][hapmap];0.90[GIH][hapmap];0.86[TSI][hapmap];0.88[EUR][1000 genomes]
rs488271	0.96[CEU][hapmap];0.88[EUR][1000 genomes]
rs4926422	0.84[EUR][1000 genomes]
rs494952	0.82[EUR][1000 genomes]
rs497128	0.83[EUR][1000 genomes]
rs519126	0.86[EUR][1000 genomes]
rs543179	0.88[EUR][1000 genomes]
rs573351	0.81[EUR][1000 genomes]
rs578353	0.96[CEU][hapmap];0.90[GIH][hapmap];0.89[TSI][hapmap];0.87[EUR][1000 genomes]
rs580159	0.88[EUR][1000 genomes]
rs6678973	0.80[AMR][1000 genomes]
rs6685252	0.94[EUR][1000 genomes]
rs6693697	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs696615	0.83[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];0.91[JPT][hapmap];0.83[MEX][hapmap];0.89[TSI][hapmap];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs696617	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs698913	0.96[CEU][hapmap]
rs698914	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs698917	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs698921	0.91[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];0.91[JPT][hapmap];0.83[MEX][hapmap];0.89[TSI][hapmap];0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs698922	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7411534	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];0.86[JPT][hapmap];0.86[LWK][hapmap];0.87[MEX][hapmap];0.84[MKK][hapmap];0.86[TSI][hapmap];0.84[YRI][hapmap]
rs7513182	0.95[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap]
rs7544900	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7548085	0.95[CEU][hapmap]
rs7554686	0.95[CEU][hapmap];0.90[EUR][1000 genomes]
rs8006	0.96[CEU][hapmap];0.88[EUR][1000 genomes]
rs828784	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs834225	0.91[ASW][hapmap];0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];0.91[JPT][hapmap];0.82[LWK][hapmap];0.83[MEX][hapmap];0.89[TSI][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs834234	0.96[CEU][hapmap];0.90[GIH][hapmap];0.89[TSI][hapmap]
rs834235	0.96[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs834237	0.96[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs834238	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];0.91[JPT][hapmap];0.83[MEX][hapmap];0.87[TSI][hapmap];0.80[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs834242	0.96[CEU][hapmap];0.90[GIH][hapmap];0.87[TSI][hapmap]
rs834243	0.82[EUR][1000 genomes]
rs863862	0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs9126	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]

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	nsv529719	chr1:150006344-150311095	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	100 gene(s)	inside rSNPs	diseases
2	nsv916014	chr1:150187139-150537483	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	164 gene(s)	inside rSNPs	diseases
3	nsv1009508	chr1:150211112-150270830	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription 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 target site	36 gene(s)	inside rSNPs	diseases
4	nsv535154	chr1:150214907-150265508	Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	nsv1011223	chr1:150229205-150279380	Active TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs10157197	PRUNE	cis	cerebellum	SCAN
rs10157197	CRCT1	cis	parietal	SCAN
rs10157197	MRPS21	cis	parietal	SCAN
rs10157197	MRPS21	cis	Thyroid	GTEx
rs10157197	MRPS21	cis	cerebellum	SCAN

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:150241800-150253400	Weak transcription	Ovary	ovary
2	chr1:150241800-150253800	Weak transcription	Esophagus	oesophagus
3	chr1:150241800-150253800	Weak transcription	Gastric	stomach
4	chr1:150241800-150254200	Weak transcription	Spleen	Spleen
5	chr1:150242000-150253400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr1:150242000-150253800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr1:150242200-150252600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr1:150242200-150253200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr1:150242200-150253200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr1:150242200-150253400	Weak transcription	Primary T cells from cord blood	blood
11	chr1:150242200-150253400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
12	chr1:150242400-150253000	Weak transcription	Primary T cells fromperipheralblood	blood
13	chr1:150242400-150253200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
14	chr1:150242600-150253200	Weak transcription	Primary T helper cells PMA-I stimulated	--
15	chr1:150245400-150253600	Weak transcription	Brain Angular Gyrus	brain
16	chr1:150245600-150252800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr1:150245600-150252800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr1:150245600-150252800	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr1:150245600-150253200	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr1:150245600-150253400	Weak transcription	Placenta	Placenta
21	chr1:150245600-150253800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr1:150245600-150253800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr1:150245600-150253800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
24	chr1:150245600-150253800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr1:150245600-150254200	Weak transcription	Lung	lung
26	chr1:150245800-150252600	Weak transcription	Rectal Mucosa Donor 29	rectum
27	chr1:150245800-150252800	Weak transcription	Skeletal Muscle Female	skeletal muscle
28	chr1:150245800-150253400	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr1:150245800-150253800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr1:150245800-150253800	Weak transcription	Left Ventricle	heart
31	chr1:150245800-150253800	Weak transcription	Right Ventricle	heart
32	chr1:150245800-150254000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr1:150246000-150252400	Weak transcription	Fetal Intestine Large	intestine
34	chr1:150246000-150252400	Weak transcription	Stomach Smooth Muscle	stomach
35	chr1:150246000-150253400	Weak transcription	HUES48 Cell Line	embryonic stem cell
36	chr1:150246000-150253400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr1:150246000-150253800	Weak transcription	H9 Cell Line	embryonic stem cell
38	chr1:150246000-150254000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr1:150246200-150253400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr1:150246200-150253400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
41	chr1:150246200-150253400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr1:150246200-150253600	Weak transcription	Fetal Kidney	kidney
43	chr1:150246200-150254000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr1:150246400-150250800	Weak transcription	Fetal Muscle Leg	muscle
45	chr1:150246400-150251600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr1:150246400-150252200	Weak transcription	Colonic Mucosa	Colon
47	chr1:150246400-150252800	Weak transcription	Brain Anterior Caudate	brain
48	chr1:150246400-150252800	Weak transcription	Right Atrium	heart
49	chr1:150246400-150252800	Weak transcription	NHDF-Ad	bronchial
50	chr1:150246400-150253000	Weak transcription	NHLF	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links