Variant report

Variant	rs13079407
Chromosome Location	chr3:47861575-47861576
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:47859202-47861700	K562	blood:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:47851874..47854469-chr3:47860393..47862264,2	MCF-7	breast:
2	chr3:47855333..47857143-chr3:47860194..47862365,2	MCF-7	breast:
3	chr3:47851691..47863624-chr3:47863694..47870558,21	K562	blood:
4	chr3:47859553..47862353-chr3:47863796..47868365,4	K562	blood:
5	chr3:47844071..47846610-chr3:47860071..47863665,3	K562	blood:

No data

Variant related genes	Relation type
DHX30	TF binding region
ENSG00000132153	Chromatin interaction

Extended variants
information (count: 138 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:136)

rs_ID	r²[population]
rs1013431	0.91[CEU][hapmap]
rs1060407	0.91[CEU][hapmap]
rs1061003	0.88[AFR][1000 genomes]
rs11130144	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs11130145	0.83[AMR][1000 genomes]
rs11130146	1.00[CEU][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes]
rs11130147	0.83[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs11130148	1.00[CEU][hapmap]
rs11130150	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11130152	0.91[CEU][hapmap];0.96[YRI][hapmap]
rs11707679	0.91[CEU][hapmap]
rs11708849	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11710199	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11712464	1.00[CEU][hapmap]
rs11714942	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs12492915	0.80[AMR][1000 genomes]
rs12495204	0.95[CEU][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs12497921	0.80[AMR][1000 genomes]
rs12498027	0.82[AMR][1000 genomes]
rs12633604	0.81[AMR][1000 genomes]
rs12635438	1.00[CEU][hapmap]
rs13061412	1.00[CEU][hapmap];0.81[AMR][1000 genomes]
rs13063042	1.00[CEU][hapmap];0.96[YRI][hapmap];0.82[AMR][1000 genomes]
rs13064183	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs13070035	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs13074973	0.92[CEU][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes]
rs13077230	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13081356	0.83[AMR][1000 genomes]
rs13086149	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13091913	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13094264	1.00[CEU][hapmap]
rs13098128	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1486915	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1684942	1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs17079785	1.00[CEU][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs17290490	1.00[CEU][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2030596	0.80[AMR][1000 genomes]
rs2047559	1.00[CEU][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs2053767	0.80[AFR][1000 genomes]
rs2101398	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2121754	0.91[CEU][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes]
rs2133601	0.91[CEU][hapmap];0.96[YRI][hapmap];0.82[AMR][1000 genomes]
rs2140335	1.00[CEU][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes]
rs2166770	0.91[CEU][hapmap]
rs2351248	0.87[CEU][hapmap]
rs2631721	0.86[AFR][1000 genomes]
rs28637561	0.80[AFR][1000 genomes]
rs2882611	1.00[CEU][hapmap]
rs2882668	0.84[AFR][1000 genomes]
rs319680	0.87[AFR][1000 genomes]
rs319682	0.91[CEU][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes]
rs319684	0.85[AFR][1000 genomes]
rs319685	0.83[AFR][1000 genomes]
rs319687	0.86[AFR][1000 genomes]
rs319689	0.86[AFR][1000 genomes]
rs319690	0.85[AFR][1000 genomes]
rs319691	0.83[AFR][1000 genomes]
rs319693	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs319694	0.91[CEU][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs319695	0.91[CEU][hapmap]
rs319696	0.92[CEU][hapmap]
rs34249203	0.82[EUR][1000 genomes]
rs34351471	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs34569417	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs34906469	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35148469	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs35582375	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35698005	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3772399	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3888	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3915654	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4858803	0.80[AMR][1000 genomes]
rs4858810	0.87[CEU][hapmap]
rs4858846	1.00[CEU][hapmap];0.92[YRI][hapmap];0.82[AMR][1000 genomes]
rs4858851	1.00[CEU][hapmap]
rs4858853	0.83[EUR][1000 genomes]
rs4858857	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4858860	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4858863	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs4858871	0.91[CEU][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs55823596	0.82[EUR][1000 genomes]
rs61181421	0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62262129	0.81[AMR][1000 genomes]
rs62263561	0.82[EUR][1000 genomes]
rs62263575	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6442074	0.82[AMR][1000 genomes]
rs6442082	1.00[CEU][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs6442083	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs6442085	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6442086	0.85[EUR][1000 genomes]
rs6442090	0.80[AFR][1000 genomes]
rs6768699	1.00[CEU][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs6770467	0.80[AFR][1000 genomes]
rs6770477	0.80[AFR][1000 genomes]
rs6772301	1.00[CEU][hapmap];0.93[YRI][hapmap];0.82[AMR][1000 genomes]
rs6772396	0.82[AFR][1000 genomes]
rs6776963	0.95[CEU][hapmap];0.86[EUR][1000 genomes]
rs6777632	1.00[CEU][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6785669	1.00[CEU][hapmap]
rs6786001	1.00[CEU][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs6792350	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6792497	1.00[CEU][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes]
rs6792737	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs6806860	0.90[CEU][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs72906488	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs73085151	0.82[EUR][1000 genomes]
rs7374516	0.91[CEU][hapmap]
rs7426976	0.86[CEU][hapmap]
rs7427418	0.82[CEU][hapmap];0.96[YRI][hapmap];0.80[AFR][1000 genomes]
rs7429162	1.00[CEU][hapmap]
rs7430879	0.91[CEU][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes]
rs7430913	0.90[CEU][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs7612219	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs7613934	1.00[CEU][hapmap];1.00[YRI][hapmap];0.80[AMR][1000 genomes]
rs7618758	1.00[CEU][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs7619882	0.85[AFR][1000 genomes]
rs7621236	1.00[CEU][hapmap];1.00[YRI][hapmap];0.80[AMR][1000 genomes]
rs7624474	1.00[CEU][hapmap];1.00[YRI][hapmap];0.80[AMR][1000 genomes]
rs7629850	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs7637372	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7637950	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7638103	1.00[CEU][hapmap]
rs7645846	1.00[CEU][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs7646982	0.80[AMR][1000 genomes]
rs7649981	0.80[AFR][1000 genomes]
rs7653368	0.83[AFR][1000 genomes]
rs777015	0.91[CEU][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs796566	0.91[CEU][hapmap]
rs800762	0.87[AFR][1000 genomes]
rs810334	0.91[CEU][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs9681917	1.00[CEU][hapmap]
rs9757517	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9811277	0.80[AFR][1000 genomes]
rs9814961	0.80[AFR][1000 genomes]
rs9850154	0.87[EUR][1000 genomes]
rs9862913	0.91[CEU][hapmap]

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	nsv1003072	chr3:47673628-47869154	Enhancers Strong transcription Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
2	nsv834679	chr3:47749475-47924006	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	167 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs13079407	MRPS18AP1	cis	Muscle Skeletal	GTEx
rs13079407	MAP4	Cis_1M	lymphoblastoid	RTeQTL
rs13079407	ZNF589	cis	Nerve Tibial	GTEx
rs13079407	MRPS18AP1	cis	Nerve Tibial	GTEx
rs13079407	DHX30	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:47845600-47866000	Weak transcription	Right Atrium	heart
2	chr3:47845600-47866200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr3:47845600-47866600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr3:47845800-47866000	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr3:47846400-47863800	Strong transcription	HUES64 Cell Line	embryonic stem cell
6	chr3:47846400-47865800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr3:47846600-47863800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
8	chr3:47846600-47863800	Strong transcription	Fetal Thymus	thymus
9	chr3:47846600-47864000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
10	chr3:47846600-47864000	Strong transcription	Fetal Muscle Leg	muscle
11	chr3:47846600-47864200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr3:47846600-47864200	Strong transcription	Fetal Muscle Trunk	muscle
13	chr3:47846600-47865800	Weak transcription	Fetal Heart	heart
14	chr3:47846800-47863800	Strong transcription	HUES48 Cell Line	embryonic stem cell
15	chr3:47846800-47864400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr3:47846800-47864600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr3:47846800-47864800	Strong transcription	Fetal Stomach	stomach
18	chr3:47846800-47865800	Weak transcription	Hela-S3	cervix
19	chr3:47847000-47862400	Strong transcription	Dnd41	blood
20	chr3:47847000-47864000	Strong transcription	Cortex derived primary cultured neurospheres	brain
21	chr3:47847000-47864000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr3:47848000-47863400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr3:47848200-47864000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr3:47848600-47861600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr3:47848600-47862400	Strong transcription	Primary T helper cells fromperipheralblood	blood
26	chr3:47848600-47864000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr3:47848600-47864400	Strong transcription	Thymus	Thymus
28	chr3:47850800-47862400	Strong transcription	Monocytes-CD14+_RO01746	blood
29	chr3:47851200-47862600	Strong transcription	Primary B cells from peripheral blood	blood
30	chr3:47851200-47863800	Strong transcription	Stomach Smooth Muscle	stomach
31	chr3:47851600-47862200	Strong transcription	Lung	lung
32	chr3:47852600-47866200	Weak transcription	Psoas Muscle	Psoas
33	chr3:47853000-47865800	Weak transcription	K562	blood
34	chr3:47853000-47866000	Weak transcription	Small Intestine	intestine
35	chr3:47853200-47865800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
36	chr3:47853200-47865800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
37	chr3:47853200-47865800	Weak transcription	GM12878-XiMat	blood
38	chr3:47853200-47865800	Weak transcription	HUVEC	blood vessel
39	chr3:47853200-47866000	Weak transcription	Placenta Amnion	Placenta Amnion
40	chr3:47853400-47865200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
41	chr3:47853400-47865800	Weak transcription	Fetal Brain Male	brain
42	chr3:47853400-47865800	Weak transcription	Stomach Mucosa	stomach
43	chr3:47855200-47864800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr3:47856200-47862400	Strong transcription	Primary T cells from cord blood	blood
45	chr3:47856200-47863600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr3:47856200-47863800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
47	chr3:47856200-47864000	Strong transcription	Fetal Intestine Large	intestine
48	chr3:47856400-47862400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr3:47856400-47862400	Strong transcription	Liver	Liver
50	chr3:47856400-47862400	Strong transcription	Duodenum Mucosa	Duodenum

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