Variant report

Variant	rs11121555
Chromosome Location	chr1:10442856-10442857
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:10440159..10442885-chr1:10447718..10449584,2	MCF-7	breast:
2	chr1:10437257..10440735-chr1:10442033..10443790,3	K562	blood:
3	chr1:10438971..10445404-chr1:10456959..10461376,9	MCF-7	breast:
4	chr1:10440809..10443662-chr1:10447796..10449625,2	MCF-7	breast:
5	chr1:10437257..10439164-chr1:10442143..10445375,4	K562	blood:
6	chr1:10440249..10443281-chr1:10456910..10459943,3	K562	blood:

Variant related genes	Relation type
ENSG00000142657	Chromatin interaction

Extended variants
information (count: 118 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:113)

rs_ID	r²[population]
rs1002076	0.90[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs10492969	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10492971	0.90[CHB][hapmap];0.95[JPT][hapmap]
rs10492972	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs10492973	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs10864450	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10864453	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs11121541	0.82[EUR][1000 genomes]
rs11121551	0.90[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs11121557	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11121560	0.86[ASN][1000 genomes]
rs11121561	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11121563	0.91[ASN][1000 genomes]
rs11121566	0.88[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1138791	0.93[ASN][1000 genomes]
rs11576384	0.85[ASN][1000 genomes]
rs11579365	0.85[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs11582123	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs11585794	0.95[CHB][hapmap];0.86[JPT][hapmap];0.93[ASN][1000 genomes]
rs11586842	0.91[ASN][1000 genomes]
rs11587309	0.95[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs11587495	0.95[CHB][hapmap];0.81[JPT][hapmap];0.92[ASN][1000 genomes]
rs11587854	0.93[ASN][1000 genomes]
rs12118323	0.86[ASN][1000 genomes]
rs12120042	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs12120191	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs12127604	0.94[CHB][hapmap];0.95[JPT][hapmap]
rs12128374	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12130563	0.95[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs12131441	0.90[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs12133617	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12141201	0.93[ASN][1000 genomes]
rs12141246	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs12141416	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs12402723	0.81[EUR][1000 genomes]
rs12409754	0.95[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs12737239	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs12738317	0.81[ASN][1000 genomes]
rs12746471	0.89[ASN][1000 genomes]
rs12757288	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs1467653	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1536262	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1538557	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs1555849	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs1556916	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs1556917	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs17034643	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs17034821	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs17402762	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17410217	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs2027330	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs2039778	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs2148152	0.82[ASN][1000 genomes]
rs2182326	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs2185252	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs2229687	0.86[ASN][1000 genomes]
rs2236678	0.86[ASN][1000 genomes]
rs34045426	0.84[ASN][1000 genomes]
rs34075302	0.80[ASN][1000 genomes]
rs34636442	0.81[ASN][1000 genomes]
rs35716098	0.86[ASN][1000 genomes]
rs35759975	0.86[ASN][1000 genomes]
rs35811280	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3737155	0.85[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs3748575	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3748577	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs3748579	0.81[ASN][1000 genomes]
rs3748581	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3762286	0.86[ASN][1000 genomes]
rs3762287	0.84[ASN][1000 genomes]
rs3762288	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4240911	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs4333852	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs4475756	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs4529713	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs4623	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs4845930	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4846197	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs4846198	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4846199	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs4846207	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs4846209	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs4846212	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs4846216	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4846218	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4846219	0.88[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4846221	0.88[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs58014725	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61326491	0.80[ASN][1000 genomes]
rs61778399	0.82[ASN][1000 genomes]
rs61778401	0.82[ASN][1000 genomes]
rs61778402	0.82[ASN][1000 genomes]
rs61778404	0.89[ASN][1000 genomes]
rs6541085	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6541089	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs6541090	0.83[EUR][1000 genomes]
rs6541094	0.88[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6674949	0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6682868	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6696056	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs746881	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs7546364	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs7546368	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7553228	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs7553935	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs8019	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs912962	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs912963	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs9332414	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs946501	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs946503	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs946504	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9651117	0.84[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	esv2757722	chr1:10238070-10582554	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	esv2758920	chr1:10238070-10582554	Strong transcription Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv817370	chr1:10305470-10697150	Weak transcription Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	nsv1008021	chr1:10363794-10802633	Strong transcription Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
5	esv2764192	chr1:10383734-10594186	Strong transcription Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11121555	PGD	cis	multi-tissue	Pritchard
rs11121555	PGD	cis	Muscle Skeletal	GTEx
rs11121555	PGD	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:10393800-10444600	Strong transcription	Cortex derived primary cultured neurospheres	brain
2	chr1:10400600-10446400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:10400600-10447400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr1:10409800-10447400	Weak transcription	Small Intestine	intestine
5	chr1:10418400-10445600	Strong transcription	Fetal Brain Female	brain
6	chr1:10420200-10445000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr1:10420200-10446000	Strong transcription	Brain Germinal Matrix	brain
8	chr1:10422400-10447200	Weak transcription	Fetal Heart	heart
9	chr1:10425800-10447800	Weak transcription	Psoas Muscle	Psoas
10	chr1:10430400-10443800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
11	chr1:10431200-10444800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr1:10434400-10447400	Weak transcription	HMEC	breast
13	chr1:10435400-10447800	Weak transcription	Primary B cells from peripheral blood	blood
14	chr1:10435400-10448000	Weak transcription	Primary T helper cells fromperipheralblood	blood
15	chr1:10435600-10443200	Weak transcription	Fetal Brain Male	brain
16	chr1:10435600-10444400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr1:10435600-10447400	Weak transcription	Aorta	Aorta
18	chr1:10435600-10447600	Weak transcription	Thymus	Thymus
19	chr1:10435600-10448800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr1:10435600-10448800	Weak transcription	Gastric	stomach
21	chr1:10435800-10448000	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr1:10436800-10448400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr1:10437000-10447800	Weak transcription	Left Ventricle	heart
24	chr1:10437000-10448000	Weak transcription	Primary T helper cells PMA-I stimulated	--
25	chr1:10437400-10447000	Weak transcription	Dnd41	blood
26	chr1:10437400-10447600	Weak transcription	Primary hematopoietic stem cells	blood
27	chr1:10437600-10443600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr1:10437600-10447800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
29	chr1:10438600-10445800	Strong transcription	Fetal Muscle Leg	muscle
30	chr1:10438600-10447000	Weak transcription	Primary B cells from cord blood	blood
31	chr1:10438600-10458200	Weak transcription	Right Atrium	heart
32	chr1:10438800-10445400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr1:10438800-10445400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr1:10438800-10446400	Weak transcription	Hela-S3	cervix
35	chr1:10438800-10447600	Weak transcription	Fetal Kidney	kidney
36	chr1:10438800-10448000	Weak transcription	Spleen	Spleen
37	chr1:10439000-10447600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr1:10439000-10448200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr1:10439200-10447200	Weak transcription	Fetal Lung	lung
40	chr1:10439200-10447200	Weak transcription	Skeletal Muscle Male	skeletal muscle
41	chr1:10439200-10447600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
42	chr1:10439400-10446400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr1:10439400-10447000	Weak transcription	Fetal Thymus	thymus
44	chr1:10439400-10447000	Weak transcription	NHEK	skin
45	chr1:10439400-10447400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr1:10439600-10445200	Weak transcription	HepG2	liver
47	chr1:10439600-10447000	Weak transcription	Colon Smooth Muscle	Colon
48	chr1:10439600-10447000	Weak transcription	Rectal Mucosa Donor 31	rectum
49	chr1:10439600-10447200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
50	chr1:10439600-10447400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links