Variant report

Variant	rs10908479
Chromosome Location	chr1:155643403-155643404
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 76 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10752611	0.96[CEU][hapmap];0.81[CHB][hapmap];0.91[JPT][hapmap];0.84[EUR][1000 genomes]
rs10908469	0.92[CEU][hapmap];0.92[JPT][hapmap]
rs10908470	0.96[CEU][hapmap];0.81[CHB][hapmap];0.91[JPT][hapmap];0.86[EUR][1000 genomes]
rs10908471	0.96[CEU][hapmap];0.92[JPT][hapmap];0.87[EUR][1000 genomes]
rs10908472	0.87[EUR][1000 genomes]
rs10908481	0.88[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap]
rs11264380	0.96[CEU][hapmap];0.81[CHB][hapmap];0.91[JPT][hapmap];0.84[EUR][1000 genomes]
rs11264381	0.96[CEU][hapmap];0.85[CHB][hapmap];0.91[JPT][hapmap];0.82[EUR][1000 genomes]
rs11264383	0.87[EUR][1000 genomes]
rs11264386	0.90[EUR][1000 genomes]
rs11264387	0.96[CEU][hapmap];0.81[CHB][hapmap];0.91[EUR][1000 genomes]
rs11264393	0.93[EUR][1000 genomes]
rs11264397	0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11264398	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12022088	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12030596	0.86[EUR][1000 genomes]
rs12035524	0.84[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12039893	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12040100	0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12047626	0.91[EUR][1000 genomes]
rs12047756	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12079134	0.92[CEU][hapmap];0.92[JPT][hapmap]
rs12093350	0.86[EUR][1000 genomes]
rs12143948	0.81[CHB][hapmap];0.91[JPT][hapmap]
rs12740629	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12744132	0.84[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12746592	0.96[CEU][hapmap];0.81[CHB][hapmap];0.91[JPT][hapmap];0.82[EUR][1000 genomes]
rs12758945	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1360554	0.81[CHB][hapmap];0.91[JPT][hapmap]
rs1556488	0.96[CEU][hapmap];0.81[JPT][hapmap]
rs2048431	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2175391	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2666826	0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs28662267	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs34124416	0.94[EUR][1000 genomes]
rs34620961	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs348186	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs348192	0.84[AMR][1000 genomes]
rs348196	0.84[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35615695	0.81[CHB][hapmap];0.91[JPT][hapmap]
rs3738590	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3820594	0.92[CEU][hapmap];0.80[CHB][hapmap];0.82[JPT][hapmap]
rs3851912	0.94[EUR][1000 genomes]
rs3892792	0.96[CEU][hapmap];0.81[CHB][hapmap];0.93[JPT][hapmap];0.89[EUR][1000 genomes]
rs4550031	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs475550	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs490608	0.82[ASN][1000 genomes]
rs4971095	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6427278	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6427286	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs644853	0.84[JPT][hapmap]
rs6672128	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6688636	0.81[CHB][hapmap];0.91[JPT][hapmap]
rs6696888	0.81[CHB][hapmap];0.91[JPT][hapmap]
rs670876	0.84[CEU][hapmap];0.91[CHB][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs678157	0.84[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs708611	0.85[CHB][hapmap]
rs7411786	0.84[EUR][1000 genomes]
rs7521594	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7541060	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs821551	0.91[JPT][hapmap]
rs822490	0.80[CHB][hapmap];0.82[JPT][hapmap]
rs860295	0.85[CHB][hapmap];0.82[JPT][hapmap]
rs9426933	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529709	chr1:155154933-155757219	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	450 gene(s)	inside rSNPs	diseases
2	esv33869	chr1:155223283-155917961	Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	187 gene(s)	inside rSNPs	diseases
3	esv3431739	chr1:155514331-155664183	Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer 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	61 gene(s)	inside rSNPs	diseases
4	esv3388968	chr1:155532335-155658278	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
5	nsv1002390	chr1:155553423-155706930	Strong transcription Weak transcription Enhancers Flanking Active TSS 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	42 gene(s)	inside rSNPs	diseases
6	nsv428246	chr1:155558197-155785831	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
7	nsv436522	chr1:155559513-155674249	Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Weak transcription 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 target site	40 gene(s)	inside rSNPs	diseases
8	esv3360339	chr1:155562157-155683127	Active TSS Flanking Active TSS Genic enhancers Enhancers Strong transcription ZNF genes & repeats Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
9	nsv547965	chr1:155563152-155688600	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
10	esv3381327	chr1:155582853-155718436	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
11	esv3436971	chr1:155618172-155733386	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
12	esv3338099	chr1:155618190-155733359	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10908479	RIT1	Cis_1M	lymphoblastoid	RTeQTL
rs10908479	FDPS	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:155627000-155657600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr1:155627200-155648200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr1:155627200-155651600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr1:155627200-155654000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr1:155627600-155650200	Strong transcription	GM12878-XiMat	blood
6	chr1:155627600-155650600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr1:155627600-155653600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr1:155627800-155650600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr1:155628000-155647600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr1:155628000-155648000	Strong transcription	Primary hematopoietic stem cells	blood
11	chr1:155628000-155650400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr1:155628000-155650400	Strong transcription	Duodenum Smooth Muscle	Duodenum
13	chr1:155628000-155650400	Strong transcription	Stomach Smooth Muscle	stomach
14	chr1:155628000-155650600	Strong transcription	HUES6 Cell Line	embryonic stem cell
15	chr1:155628000-155650600	Strong transcription	Primary B cells from peripheral blood	blood
16	chr1:155628000-155650600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
17	chr1:155628000-155650600	Strong transcription	Sigmoid Colon	Sigmoid Colon
18	chr1:155628000-155650800	Strong transcription	Primary T cells from cord blood	blood
19	chr1:155628000-155650800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr1:155628000-155650800	Strong transcription	Placenta	Placenta
21	chr1:155628000-155651600	Strong transcription	Adipose Nuclei	Adipose
22	chr1:155628000-155652000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
23	chr1:155628000-155652000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr1:155628000-155653800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr1:155628000-155654600	Strong transcription	Fetal Thymus	thymus
26	chr1:155628200-155645400	Strong transcription	Primary monocytes fromperipheralblood	blood
27	chr1:155628200-155645600	Strong transcription	Monocytes-CD14+_RO01746	blood
28	chr1:155628200-155647000	Strong transcription	Cortex derived primary cultured neurospheres	brain
29	chr1:155628200-155649600	Strong transcription	Brain Cingulate Gyrus	brain
30	chr1:155628200-155649800	Strong transcription	Osteobl	bone
31	chr1:155628200-155650200	Strong transcription	HUES48 Cell Line	embryonic stem cell
32	chr1:155628200-155650200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr1:155628200-155650200	Strong transcription	Fetal Intestine Large	intestine
34	chr1:155628200-155650400	Strong transcription	HUES64 Cell Line	embryonic stem cell
35	chr1:155628200-155650400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
36	chr1:155628200-155650400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr1:155628200-155650600	Strong transcription	Primary T helper naive cells from peripheral blood	blood
38	chr1:155628200-155650600	Strong transcription	Brain Inferior Temporal Lobe	brain
39	chr1:155628200-155650800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
40	chr1:155628200-155650800	Strong transcription	Primary T helper cells fromperipheralblood	blood
41	chr1:155628200-155650800	Strong transcription	Duodenum Mucosa	Duodenum
42	chr1:155628200-155651000	Strong transcription	Primary neutrophils fromperipheralblood	blood
43	chr1:155628200-155651000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr1:155628200-155651200	Strong transcription	Primary T helper cells PMA-I stimulated	--
45	chr1:155628200-155651200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
46	chr1:155628200-155653200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
47	chr1:155628400-155645200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr1:155628400-155647200	Strong transcription	Skeletal Muscle Male	skeletal muscle
49	chr1:155628400-155648200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr1:155628400-155649800	Strong transcription	Brain Anterior Caudate	brain

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