Variant report

Variant	rs4902418
Chromosome Location	chr14:39604335-39604336
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:39602771..39604896-chr14:39637781..39640211,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000182400	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10130972	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10133797	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10136536	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10137988	1.00[ASW][hapmap]
rs10149120	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10151683	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1061583	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap]
rs11157041	0.86[CHB][hapmap];0.80[CHD][hapmap];0.93[GIH][hapmap];0.90[MKK][hapmap]
rs12147991	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12437405	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12885242	1.00[ASW][hapmap];0.86[CHB][hapmap];0.93[GIH][hapmap];1.00[LWK][hapmap];0.82[MEX][hapmap];0.96[MKK][hapmap]
rs12890771	1.00[ASW][hapmap]
rs12891258	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12894046	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12895751	0.81[EUR][1000 genomes]
rs13379360	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17108846	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2737721	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2737729	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2753606	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28379470	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28485301	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2869	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28856917	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34816815	0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35035794	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3742354	1.00[ASW][hapmap];0.93[CHB][hapmap];0.81[CHD][hapmap];0.93[GIH][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];0.90[TSI][hapmap]
rs3759545	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4143954	0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4902405	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4902406	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4902431	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4902435	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4902448	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs532	0.81[EUR][1000 genomes]
rs58851254	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs67248626	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs71407780	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7147194	0.90[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7153124	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8006879	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8009933	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs9322992	0.86[CHB][hapmap]
rs9322994	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]

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	esv3429206	chr14:39160730-39648836	Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
2	nsv1051247	chr14:39604035-39652789	Genic enhancers Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' 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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4902418	TRAPPC6B	cis	multi-tissue	Pritchard
rs4902418	SIP1	Cis_1M	lymphoblastoid	RTeQTL
rs4902418	SSTR1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:39583800-39626000	Weak transcription	Spleen	Spleen
2	chr14:39584000-39615000	Weak transcription	Pancreas	Pancrea
3	chr14:39584000-39623600	Weak transcription	Esophagus	oesophagus
4	chr14:39584200-39610800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr14:39584200-39636000	Weak transcription	Small Intestine	intestine
6	chr14:39584200-39638600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr14:39584400-39617200	Weak transcription	Psoas Muscle	Psoas
8	chr14:39584400-39620800	Weak transcription	Colonic Mucosa	Colon
9	chr14:39584400-39626600	Weak transcription	Aorta	Aorta
10	chr14:39584600-39604600	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr14:39584600-39609600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr14:39584600-39625800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr14:39585200-39608200	Strong transcription	HUES6 Cell Line	embryonic stem cell
14	chr14:39585800-39608200	Strong transcription	HUES48 Cell Line	embryonic stem cell
15	chr14:39586000-39608000	Strong transcription	HUES64 Cell Line	embryonic stem cell
16	chr14:39586000-39608400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr14:39586000-39608600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr14:39586000-39608800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr14:39586600-39610600	Strong transcription	HepG2	liver
20	chr14:39587200-39609600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr14:39587400-39608400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr14:39587600-39607800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr14:39588600-39635400	Weak transcription	Fetal Brain Male	brain
24	chr14:39589200-39604800	Weak transcription	HSMMtube	muscle
25	chr14:39589200-39609200	Weak transcription	Gastric	stomach
26	chr14:39589200-39610000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr14:39589200-39618000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
28	chr14:39589200-39626400	Weak transcription	Fetal Heart	heart
29	chr14:39591800-39606600	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr14:39592600-39605200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
31	chr14:39592600-39622200	Weak transcription	Right Ventricle	heart
32	chr14:39592800-39606600	Weak transcription	Brain Cingulate Gyrus	brain
33	chr14:39592800-39607400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr14:39592800-39618000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
35	chr14:39592800-39626600	Weak transcription	NHLF	lung
36	chr14:39593400-39604800	Weak transcription	H9 Cell Line	embryonic stem cell
37	chr14:39594000-39620800	Weak transcription	Hela-S3	cervix
38	chr14:39594600-39606600	Weak transcription	Fetal Kidney	kidney
39	chr14:39594800-39608000	Weak transcription	Brain Angular Gyrus	brain
40	chr14:39596200-39621200	Weak transcription	Brain Substantia Nigra	brain
41	chr14:39596400-39607400	Weak transcription	Brain Anterior Caudate	brain
42	chr14:39596800-39608200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr14:39596800-39608600	Strong transcription	Primary monocytes fromperipheralblood	blood
44	chr14:39597200-39608000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
45	chr14:39597400-39608200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
46	chr14:39597800-39607200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr14:39597800-39610000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr14:39598000-39612600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr14:39598200-39608000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr14:39598400-39604800	Weak transcription	Placenta Amnion	Placenta Amnion

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