Variant report

Variant	rs11121566
Chromosome Location	chr1:10472848-10472849
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:10472803-10473391	A549	lung:	n/a	n/a
2	POLR2A	chr1:10463619-10473680	A549	lung:	n/a	n/a
3	POLR2A	chr1:10471633-10473588	K562	blood:	n/a	n/a
4	POLR2A	chr1:10472745-10473101	A549	lung:	n/a	n/a
5	POLR2A	chr1:10472729-10473052	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:10457490..10461716-chr1:10469511..10473951,6	K562	blood:
2	chr1:10449520..10451785-chr1:10471449..10473119,2	K562	blood:

Variant related genes	Relation type
PGD	TF binding region
ENSG00000142657	Chromatin interaction
ENSG00000265945	Chromatin interaction

Extended variants
information (count: 119 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:109)

rs_ID	r²[population]
rs1002076	0.80[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs10492969	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs10492971	0.95[JPT][hapmap]
rs10492972	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs10492973	0.85[CHB][hapmap];0.95[JPT][hapmap]
rs10864450	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs10864453	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs11121541	0.83[EUR][1000 genomes]
rs11121543	0.83[YRI][hapmap]
rs11121551	0.80[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs11121555	0.88[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11121557	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11121560	0.91[ASN][1000 genomes]
rs11121561	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11121563	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1138791	0.90[ASN][1000 genomes]
rs11576384	0.96[ASN][1000 genomes]
rs11579365	0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs11582123	0.85[CHB][hapmap];0.95[JPT][hapmap]
rs11585794	0.85[CHB][hapmap];0.86[JPT][hapmap];0.90[ASN][1000 genomes]
rs11586842	0.87[ASN][1000 genomes]
rs11587309	0.85[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs11587495	0.84[CHB][hapmap];0.81[JPT][hapmap];0.88[ASN][1000 genomes]
rs11587854	0.90[ASN][1000 genomes]
rs12064209	0.83[YRI][hapmap]
rs12069853	0.83[YRI][hapmap]
rs12118323	0.97[ASN][1000 genomes]
rs12120042	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs12120191	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs12127604	0.89[CHB][hapmap];0.95[JPT][hapmap]
rs12128374	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12130563	0.85[CHB][hapmap];0.95[JPT][hapmap]
rs12131441	0.80[CHB][hapmap];1.00[JPT][hapmap]
rs12133617	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs12141201	0.90[ASN][1000 genomes]
rs12141246	0.85[CHB][hapmap];0.95[JPT][hapmap]
rs12141416	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs12402723	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12409754	0.85[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs12737239	0.84[CHB][hapmap];1.00[JPT][hapmap]
rs12746471	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12757288	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs1467653	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs1536262	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1538557	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs1555849	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs1556916	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs1556917	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs17034643	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs17034821	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs17402762	0.86[EUR][1000 genomes]
rs17410217	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs2027330	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap]
rs2039778	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs2182326	0.85[CHB][hapmap];0.95[JPT][hapmap]
rs2185252	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs2229687	0.97[ASN][1000 genomes]
rs2236678	0.97[ASN][1000 genomes]
rs34045426	0.95[ASN][1000 genomes]
rs34075302	0.90[ASN][1000 genomes]
rs35716098	0.94[ASN][1000 genomes]
rs35759975	0.97[ASN][1000 genomes]
rs35811280	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3737155	0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs3748575	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs3748577	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs3748581	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3762286	0.97[ASN][1000 genomes]
rs3762287	0.95[ASN][1000 genomes]
rs3762288	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4240911	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs4333852	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs4475756	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs4529713	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs4623	0.85[CHB][hapmap];0.95[JPT][hapmap]
rs4845930	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs4846197	0.80[CHB][hapmap];1.00[JPT][hapmap]
rs4846198	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs4846199	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap]
rs4846207	0.85[CHB][hapmap];0.95[JPT][hapmap]
rs4846209	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs4846212	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs4846216	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4846218	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4846219	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4846221	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58014725	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61778404	0.86[ASN][1000 genomes]
rs6541085	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs6541089	0.85[CHB][hapmap];0.95[JPT][hapmap]
rs6541090	0.84[EUR][1000 genomes]
rs6541094	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6674949	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6682868	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6696056	0.84[CHB][hapmap];0.90[JPT][hapmap]
rs6703708	0.83[YRI][hapmap]
rs746881	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs7546364	0.85[CHB][hapmap];0.95[JPT][hapmap]
rs7546368	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs7553228	0.85[CHB][hapmap];0.95[JPT][hapmap]
rs7553935	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs8019	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs912962	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs912963	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs9332414	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs946501	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs946503	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs946504	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs9651117	0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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
6	nsv1003498	chr1:10445928-10607351	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
7	nsv998731	chr1:10464176-10607351	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
8	esv1827009	chr1:10467074-10483456	Weak transcription Strong transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
9	esv1830329	chr1:10467074-10483456	Genic enhancers Strong transcription Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
10	esv1831760	chr1:10467074-10483456	Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Active TSS	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11121566	PGD	cis	Muscle Skeletal	GTEx
rs11121566	PGD	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:10460000-10490200	Weak transcription	Psoas Muscle	Psoas
2	chr1:10460200-10475400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr1:10460400-10475200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr1:10460600-10481200	Strong transcription	H1 Cell Line	embryonic stem cell
5	chr1:10460800-10480400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr1:10460800-10482000	Strong transcription	HUES48 Cell Line	embryonic stem cell
7	chr1:10460800-10482400	Strong transcription	Fetal Stomach	stomach
8	chr1:10460800-10483400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr1:10461000-10474600	Strong transcription	HUES6 Cell Line	embryonic stem cell
10	chr1:10461000-10475200	Strong transcription	HUES64 Cell Line	embryonic stem cell
11	chr1:10461000-10476800	Weak transcription	Fetal Heart	heart
12	chr1:10461000-10482000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
13	chr1:10461200-10482000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr1:10461200-10482000	Strong transcription	Fetal Muscle Leg	muscle
15	chr1:10461200-10490000	Weak transcription	Right Atrium	heart
16	chr1:10461400-10475200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr1:10461400-10483000	Strong transcription	Cortex derived primary cultured neurospheres	brain
18	chr1:10461400-10483000	Strong transcription	Fetal Intestine Small	intestine
19	chr1:10461400-10483400	Strong transcription	Fetal Muscle Trunk	muscle
20	chr1:10461600-10481800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
21	chr1:10461600-10482800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr1:10461800-10473600	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr1:10461800-10473600	Strong transcription	Primary hematopoietic stem cells	blood
24	chr1:10461800-10473600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr1:10461800-10473600	Strong transcription	Rectal Smooth Muscle	rectum
26	chr1:10461800-10474200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
27	chr1:10461800-10475200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr1:10461800-10482000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr1:10461800-10482000	Strong transcription	Dnd41	blood
30	chr1:10462000-10473000	Strong transcription	Primary monocytes fromperipheralblood	blood
31	chr1:10462000-10475200	Strong transcription	H9 Cell Line	embryonic stem cell
32	chr1:10462000-10482000	Strong transcription	Fetal Intestine Large	intestine
33	chr1:10462000-10482200	Strong transcription	Brain Germinal Matrix	brain
34	chr1:10462000-10483000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr1:10462200-10473200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr1:10462200-10475000	Strong transcription	iPS-15b Cell Line	embryonic stem cell
37	chr1:10462200-10475200	Strong transcription	ES-I3 Cell Line	embryonic stem cell
38	chr1:10462200-10475400	Strong transcription	Primary T helper cells PMA-I stimulated	--
39	chr1:10462200-10475400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr1:10462200-10481600	Strong transcription	Liver	Liver
41	chr1:10462200-10481600	Strong transcription	Skeletal Muscle Male	skeletal muscle
42	chr1:10462200-10482000	Strong transcription	Sigmoid Colon	Sigmoid Colon
43	chr1:10462200-10483200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr1:10462400-10476000	Strong transcription	Ovary	ovary
45	chr1:10462600-10473600	Strong transcription	Esophagus	oesophagus
46	chr1:10462600-10482000	Strong transcription	Duodenum Mucosa	Duodenum
47	chr1:10462800-10473400	Strong transcription	Primary B cells from cord blood	blood
48	chr1:10462800-10473400	Strong transcription	Lung	lung
49	chr1:10462800-10473400	Strong transcription	Right Ventricle	heart
50	chr1:10462800-10473800	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain

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