Variant report

Variant	rs2753606
Chromosome Location	chr14:39652724-39652725
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr14:39651767..39657982-chr14:39696424..39701629,5	MCF-7	breast:
2	chr14:39651871..39654162-chr6:64282576..64285387,2	MCF-7	breast:
3	chr14:39581109..39582848-chr14:39652631..39654902,2	K562	blood:
4	chr14:39651862..39654641-chr14:39690512..39693459,3	K562	blood:
5	chr14:39513894..39516551-chr14:39652021..39654125,2	K562	blood:
6	chr14:39652103..39654981-chr14:39673043..39674708,2	K562	blood:
7	chr14:39650808..39656380-chr14:39733766..39738257,10	MCF-7	breast:
8	chr14:39652084..39653603-chr14:39673208..39674961,2	K562	blood:
9	chr14:39652603..39655105-chr14:39837196..39838918,2	K562	blood:
10	chr14:39581087..39583889-chr14:39651029..39653848,3	MCF-7	breast:
11	chr14:39652070..39652832-chr2:61244630..61245448,2	Hela-S3	cervix:
12	chr14:39652053..39654773-chr14:39736732..39739387,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000092208	Chromatin interaction
ENSG00000162927	Chromatin interaction
ENSG00000258941	Chromatin interaction
ENSG00000150526	Chromatin interaction
ENSG00000112245	Chromatin interaction
ENSG00000150527	Chromatin interaction
ENSG00000258940	Chromatin interaction
ENSG00000162928	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10130972	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10133797	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10136536	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10149120	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10151683	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1061583	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11157041	0.86[CHB][hapmap]
rs12147991	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12437405	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12885242	0.86[CHB][hapmap]
rs12891258	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12894046	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13379360	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17108846	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]
rs2737721	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2737729	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28379470	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28485301	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2869	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]
rs28856917	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34816815	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35035794	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3742354	0.93[CHB][hapmap]
rs3759545	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4143954	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4902405	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4902406	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4902418	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]
rs4902431	0.91[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]
rs4902435	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4902448	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs532	0.82[CEU][hapmap];0.83[EUR][1000 genomes]
rs58851254	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67248626	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71407780	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7147194	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7153124	0.86[ASN][1000 genomes]
rs8006879	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8009933	0.83[CEU][hapmap];0.87[CHB][hapmap];0.87[JPT][hapmap]
rs9322992	0.87[CHB][hapmap]
rs9322994	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2753606	TRAPPC6B	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:39645600-39655400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr14:39645800-39653000	Strong transcription	Placenta Amnion	Placenta Amnion
3	chr14:39645800-39653400	Strong transcription	H9 Cell Line	embryonic stem cell
4	chr14:39645800-39654600	Strong transcription	Cortex derived primary cultured neurospheres	brain
5	chr14:39645800-39655200	Strong transcription	Placenta	Placenta
6	chr14:39645800-39657200	Strong transcription	HSMM	muscle
7	chr14:39646000-39652800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr14:39646000-39654200	Strong transcription	Sigmoid Colon	Sigmoid Colon
9	chr14:39646000-39654800	Strong transcription	Primary monocytes fromperipheralblood	blood
10	chr14:39646000-39654800	Strong transcription	Monocytes-CD14+_RO01746	blood
11	chr14:39646000-39655200	Strong transcription	HSMMtube	muscle
12	chr14:39646200-39653000	Strong transcription	Fetal Lung	lung
13	chr14:39646200-39654400	Strong transcription	Primary B cells from cord blood	blood
14	chr14:39646200-39654400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr14:39646200-39654400	Strong transcription	Brain Inferior Temporal Lobe	brain
16	chr14:39646200-39654600	Strong transcription	Osteobl	bone
17	chr14:39646200-39654800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr14:39646200-39654800	Strong transcription	Fetal Brain Female	brain
19	chr14:39646200-39655000	Strong transcription	Stomach Smooth Muscle	stomach
20	chr14:39646400-39653000	Strong transcription	ES-I3 Cell Line	embryonic stem cell
21	chr14:39646400-39653000	Strong transcription	Primary hematopoietic stem cells	blood
22	chr14:39646400-39653400	Strong transcription	NHDF-Ad	bronchial
23	chr14:39646400-39654200	Strong transcription	Brain Substantia Nigra	brain
24	chr14:39646400-39654400	Strong transcription	NHLF	lung
25	chr14:39646400-39654800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr14:39646400-39654800	Strong transcription	Primary neutrophils fromperipheralblood	blood
27	chr14:39646400-39654800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr14:39646400-39655000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr14:39646400-39655000	Strong transcription	HMEC	breast
30	chr14:39646400-39655200	Strong transcription	HUES48 Cell Line	embryonic stem cell
31	chr14:39646400-39655200	Strong transcription	Primary B cells from peripheral blood	blood
32	chr14:39646400-39655200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr14:39646400-39655400	Strong transcription	HUES6 Cell Line	embryonic stem cell
34	chr14:39646400-39655400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr14:39646400-39655800	Strong transcription	Fetal Thymus	thymus
36	chr14:39646600-39653200	Strong transcription	K562	blood
37	chr14:39646600-39654000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr14:39646600-39654200	Strong transcription	NHEK	skin
39	chr14:39646600-39654400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr14:39646600-39654400	Strong transcription	Rectal Mucosa Donor 31	rectum
41	chr14:39646600-39654400	Strong transcription	Skeletal Muscle Male	skeletal muscle
42	chr14:39646600-39654600	Strong transcription	Duodenum Mucosa	Duodenum
43	chr14:39646600-39654800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
44	chr14:39646600-39654800	Strong transcription	Adipose Nuclei	Adipose
45	chr14:39646600-39655000	Strong transcription	Rectal Mucosa Donor 29	rectum
46	chr14:39646600-39655000	Strong transcription	Skeletal Muscle Female	skeletal muscle
47	chr14:39646600-39655400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
48	chr14:39646800-39652800	Weak transcription	Right Atrium	heart
49	chr14:39646800-39653200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr14:39646800-39654400	Strong transcription	H1 Cell Line	embryonic stem cell

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