Variant report

Variant	rs4902405
Chromosome Location	chr14:39584464-39584465
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:39583285..39585580-chr14:39639274..39641168,2	K562	blood:
2	chr14:39583538..39585580-chr14:39639274..39642211,2	K562	blood:
3	chr14:39582528..39584759-chr14:39643385..39645029,2	K562	blood:
4	chr14:39582116..39585012-chr14:39643452..39645860,4	MCF-7	breast:
5	chr14:39582047..39584964-chr14:39643383..39645099,4	K562	blood:
6	chr14:39582622..39586619-chr14:39638047..39642701,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000182400	Chromatin interaction
ENSG00000100941	Chromatin interaction
ENSG00000259083	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10130972	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10133797	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10136536	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10140341	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10149120	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10151683	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12147991	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12437405	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12891258	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12894046	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13379360	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17108846	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2737721	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2737729	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2753606	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28379470	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28485301	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28502115	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2869	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28810420	0.81[EUR][1000 genomes]
rs28856917	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34642409	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34816815	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35035794	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35224434	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35423721	0.80[EUR][1000 genomes]
rs35992529	0.80[EUR][1000 genomes]
rs3742354	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3759545	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4143954	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4902406	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4902418	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4902431	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4902435	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4902448	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs58851254	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6571893	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs67248626	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs71407780	0.84[AMR][1000 genomes]
rs7147194	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7153124	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8006879	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9322994	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[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	nsv1038622	chr14:39423562-39604035	Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4902405	TRAPPC6B	cis	multi-tissue	Pritchard
rs4902405	SIP1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:39582400-39584600	Active TSS	HUES6 Cell Line	embryonic stem cell
2	chr14:39582800-39584600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr14:39582800-39584600	Active TSS	Pancreatic Islets	Pancreatic Islet
4	chr14:39583000-39584600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr14:39583000-39584600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr14:39583000-39584600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr14:39583000-39584600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr14:39583000-39584600	Active TSS	Stomach Smooth Muscle	stomach
9	chr14:39583000-39584600	Active TSS	K562	blood
10	chr14:39583200-39584600	Active TSS	H9 Cell Line	embryonic stem cell
11	chr14:39583200-39584600	Active TSS	HUES48 Cell Line	embryonic stem cell
12	chr14:39583200-39584600	Active TSS	HUES64 Cell Line	embryonic stem cell
13	chr14:39583200-39584600	Active TSS	iPS-20b Cell Line	embryonic stem cell
14	chr14:39583400-39584600	Active TSS	HSMM	muscle
15	chr14:39583800-39584600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
16	chr14:39583800-39584600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
17	chr14:39583800-39584600	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
18	chr14:39583800-39584600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr14:39583800-39584600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr14:39583800-39584600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr14:39583800-39585200	Flanking Active TSS	Dnd41	blood
22	chr14:39583800-39588000	Weak transcription	Gastric	stomach
23	chr14:39583800-39626000	Weak transcription	Spleen	Spleen
24	chr14:39584000-39584600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr14:39584000-39584600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr14:39584000-39584600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
27	chr14:39584000-39584600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
28	chr14:39584000-39584600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr14:39584000-39584600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr14:39584000-39584600	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
31	chr14:39584000-39584600	Flanking Active TSS	Fetal Brain Female	brain
32	chr14:39584000-39584600	Flanking Active TSS	Fetal Heart	heart
33	chr14:39584000-39584600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
34	chr14:39584000-39584600	Flanking Active TSS	Thymus	Thymus
35	chr14:39584000-39584600	Flanking Active TSS	HUVEC	blood vessel
36	chr14:39584000-39584600	Flanking Active TSS	NHEK	skin
37	chr14:39584000-39584600	Flanking Active TSS	Osteobl	bone
38	chr14:39584000-39588000	Weak transcription	Lung	lung
39	chr14:39584000-39588200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr14:39584000-39590000	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr14:39584000-39595000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr14:39584000-39615000	Weak transcription	Pancreas	Pancrea
43	chr14:39584000-39623600	Weak transcription	Esophagus	oesophagus
44	chr14:39584200-39584600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
45	chr14:39584200-39584600	Enhancers	Primary monocytes fromperipheralblood	blood
46	chr14:39584200-39584600	Enhancers	Primary neutrophils fromperipheralblood	blood
47	chr14:39584200-39584600	Enhancers	Primary B cells from peripheral blood	blood
48	chr14:39584200-39584600	Flanking Active TSS	Primary T cells fromperipheralblood	blood
49	chr14:39584200-39584600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
50	chr14:39584200-39584600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin

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