Variant report

Variant	rs10205467
Chromosome Location	chr2:114480177-114480178
allele	C/T
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	STAT3	chr2:114480174-114480332	MCF10A-Er-Src	breast:	n/a	n/a

Variant related genes	Relation type
MIR4782	TF binding region
SLC35F5	TF binding region

Extended variants
information (count: 59 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10168234	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10199704	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10200355	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10206174	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10938	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11679707	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11682259	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11688799	0.80[ASN][1000 genomes]
rs11695798	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11897553	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11901060	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12711784	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12711786	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13004622	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13006627	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13029093	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13034531	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13397540	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13405475	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13416930	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1349157	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1584434	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17048473	0.93[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2122095	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2305254	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2418915	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2418916	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs35432356	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35667749	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4849264	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4849265	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4849266	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4849269	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4849274	0.82[JPT][hapmap]
rs56213422	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56376185	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs58473055	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6542171	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6704673	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6709158	0.84[CHB][hapmap]
rs6726001	0.84[CHB][hapmap]
rs6731402	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6739072	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6741521	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67850681	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7561176	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7578249	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7586800	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7587218	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7590375	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7592689	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7600550	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs935644	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9798411	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[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	nsv1001195	chr2:114362003-114506330	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv979109	chr2:114429638-114495192	Strong transcription Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv979339	chr2:114430138-114495192	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv1009509	chr2:114432965-114557306	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
5	nsv535896	chr2:114432965-114557306	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs10205467	RPL23AP7	cis	Whole Blood	GTEx
rs10205467	DDX11L2	cis	Whole Blood	GTEx
rs10205467	PS1TP4	Cis_1M	lymphoblastoid	RTeQTL
rs10205467	RPL23AP7	Cis_1M	lymphoblastoid	RTeQTL
rs10205467	RPL23AP7	cis	Muscle Skeletal	GTEx
rs10205467	SLC35F5	Cis_1M	lymphoblastoid	RTeQTL
rs10205467	SLC35F5	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:114458200-114486200	Weak transcription	Dnd41	blood
2	chr2:114458200-114512600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr2:114458400-114484200	Weak transcription	Pancreas	Pancrea
4	chr2:114458400-114497200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr2:114458400-114500000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr2:114460200-114484200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr2:114461400-114513200	Weak transcription	Small Intestine	intestine
8	chr2:114461600-114484200	Weak transcription	Lung	lung
9	chr2:114461600-114484400	Weak transcription	Brain Cingulate Gyrus	brain
10	chr2:114461600-114499800	Weak transcription	Hela-S3	cervix
11	chr2:114462000-114497400	Weak transcription	Colonic Mucosa	Colon
12	chr2:114463000-114498800	Weak transcription	Esophagus	oesophagus
13	chr2:114464000-114484200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr2:114464000-114484200	Weak transcription	Gastric	stomach
15	chr2:114464000-114497600	Weak transcription	Right Ventricle	heart
16	chr2:114464000-114497600	Weak transcription	Spleen	Spleen
17	chr2:114464600-114484600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
18	chr2:114465200-114486400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr2:114465200-114512000	Weak transcription	Stomach Mucosa	stomach
20	chr2:114465800-114484800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr2:114467400-114497200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr2:114467600-114486200	Weak transcription	Fetal Brain Male	brain
23	chr2:114467800-114484200	Weak transcription	Aorta	Aorta
24	chr2:114468800-114512800	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr2:114469400-114510400	Strong transcription	Monocytes-CD14+_RO01746	blood
26	chr2:114469800-114482000	Strong transcription	Primary neutrophils fromperipheralblood	blood
27	chr2:114469800-114486400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
28	chr2:114470000-114497400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr2:114470000-114500200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
30	chr2:114470200-114493400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr2:114470200-114511200	Strong transcription	Primary monocytes fromperipheralblood	blood
32	chr2:114470400-114510800	Strong transcription	HSMM	muscle
33	chr2:114471000-114483200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr2:114471000-114486000	Weak transcription	K562	blood
35	chr2:114471000-114488200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr2:114471000-114495600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
37	chr2:114471000-114495600	Weak transcription	Rectal Smooth Muscle	rectum
38	chr2:114471000-114498600	Weak transcription	H1 Cell Line	embryonic stem cell
39	chr2:114471000-114500200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr2:114472000-114480800	Strong transcription	HepG2	liver
41	chr2:114472800-114486200	Weak transcription	A549	lung
42	chr2:114472800-114486600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
43	chr2:114473200-114488600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
44	chr2:114473200-114494600	Weak transcription	Fetal Heart	heart
45	chr2:114473400-114484800	Weak transcription	HMEC	breast
46	chr2:114473800-114497200	Weak transcription	NHEK	skin
47	chr2:114474200-114482600	Weak transcription	Psoas Muscle	Psoas
48	chr2:114474400-114486000	Weak transcription	GM12878-XiMat	blood
49	chr2:114474400-114494600	Weak transcription	Skeletal Muscle Male	skeletal muscle
50	chr2:114474400-114507600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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