Variant report

Variant	rs4143954
Chromosome Location	chr14:39638628-39638629
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:15)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:15 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr14:39624043..39626785-chr14:39637503..39639794,2	K562	blood:
2	chr14:39637610..39639234-chr14:39680366..39682544,2	MCF-7	breast:
3	chr14:39636723..39639312-chr14:39766672..39768267,2	MCF-7	breast:
4	chr14:39576976..39580513-chr14:39638047..39641153,4	K562	blood:
5	chr14:39631838..39633415-chr14:39636342..39639514,3	MCF-7	breast:
6	chr14:39635717..39639064-chr14:39734944..39738287,4	MCF-7	breast:
7	chr14:39602771..39604896-chr14:39637781..39640211,2	MCF-7	breast:
8	chr14:39638262..39639790-chr14:39854572..39857043,2	K562	blood:
9	chr14:39582622..39586619-chr14:39638047..39642701,6	MCF-7	breast:
10	chr14:39636108..39642775-chr14:39734196..39739360,12	MCF-7	breast:
11	chr14:39572251..39574864-chr14:39637876..39641106,3	MCF-7	breast:
12	chr14:39570654..39572608-chr14:39637696..39639686,2	K562	blood:
13	chr14:39638023..39641762-chr14:39900094..39905872,5	MCF-7	breast:
14	chr14:39560368..39562617-chr14:39637895..39640290,2	MCF-7	breast:
15	chr14:39570348..39574070-chr14:39637691..39640941,4	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000241984	Chromatin interaction
ENSG00000258651	Chromatin interaction
ENSG00000258941	Chromatin interaction
ENSG00000150527	Chromatin interaction
ENSG00000258940	Chromatin interaction
ENSG00000092208	Chromatin interaction
ENSG00000100934	Chromatin interaction
ENSG00000259100	Chromatin interaction
ENSG00000258591	Chromatin interaction
ENSG00000258671	Chromatin interaction
ENSG00000165355	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10130972	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10133797	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10136536	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.81[MEX][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10149120	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10151683	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1061583	1.00[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]
rs11157041	0.86[CHB][hapmap];0.89[GIH][hapmap]
rs12147991	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];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12437405	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12885242	0.86[CHB][hapmap];0.89[GIH][hapmap]
rs12891258	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12894046	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12895751	0.81[EUR][1000 genomes]
rs13379360	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17108846	0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.88[TSI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2737721	1.00[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];0.94[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];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2753606	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]
rs28379470	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28485301	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2869	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28856917	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34816815	0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35035794	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3742354	0.93[CHB][hapmap];0.81[CHD][hapmap];0.89[GIH][hapmap];0.85[TSI][hapmap]
rs3759545	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4902405	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4902406	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4902418	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]
rs4902431	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4902435	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4902448	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs532	0.81[CEU][hapmap];0.83[EUR][1000 genomes]
rs58851254	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62640373	0.84[AFR][1000 genomes]
rs67248626	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71407780	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7147194	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.81[MEX][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7153124	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73291567	0.84[AFR][1000 genomes]
rs73291573	0.84[AFR][1000 genomes]
rs73291583	0.84[AFR][1000 genomes]
rs73291585	0.84[AFR][1000 genomes]
rs73291588	0.84[AFR][1000 genomes]
rs8006879	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8009933	0.82[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap]
rs9322992	0.86[CHB][hapmap]
rs9322994	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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
3	esv1813567	chr14:39632114-39642840	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4143954	TRAPPC6B	cis	multi-tissue	Pritchard
rs4143954	SIP1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:39611200-39638800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr14:39627000-39638800	Weak transcription	Gastric	stomach
3	chr14:39634200-39638800	Weak transcription	Spleen	Spleen
4	chr14:39635000-39638800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr14:39635400-39638800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
6	chr14:39635600-39638800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
7	chr14:39636200-39638800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
8	chr14:39636200-39640200	Active TSS	GM12878-XiMat	blood
9	chr14:39636800-39640600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr14:39637000-39638800	Weak transcription	Stomach Mucosa	stomach
11	chr14:39637400-39638800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr14:39637400-39639200	Flanking Active TSS	Duodenum Mucosa	Duodenum
13	chr14:39637400-39640200	Active TSS	Ovary	ovary
14	chr14:39637400-39640200	Active TSS	K562	blood
15	chr14:39637400-39640600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr14:39637600-39639000	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
17	chr14:39637600-39639000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
18	chr14:39637600-39639200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr14:39637600-39639400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr14:39637600-39639400	Flanking Active TSS	Adipose Nuclei	Adipose
21	chr14:39637600-39640000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr14:39637600-39640200	Active TSS	HSMMtube	muscle
23	chr14:39637600-39640400	Active TSS	Aorta	Aorta
24	chr14:39637600-39640400	Active TSS	NHDF-Ad	bronchial
25	chr14:39637600-39640400	Active TSS	NHLF	lung
26	chr14:39637800-39639000	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr14:39637800-39639000	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
28	chr14:39637800-39639000	Flanking Active TSS	Liver	Liver
29	chr14:39637800-39639000	Flanking Active TSS	Dnd41	blood
30	chr14:39637800-39639000	Flanking Active TSS	HUVEC	blood vessel
31	chr14:39637800-39640200	Active TSS	ES-I3 Cell Line	embryonic stem cell
32	chr14:39637800-39640200	Active TSS	HUES6 Cell Line	embryonic stem cell
33	chr14:39637800-39640200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr14:39637800-39640200	Active TSS	Fetal Brain Female	brain
35	chr14:39637800-39640400	Active TSS	Psoas Muscle	Psoas
36	chr14:39637800-39640400	Active TSS	Right Atrium	heart
37	chr14:39637800-39640600	Active TSS	Brain Anterior Caudate	brain
38	chr14:39638000-39639000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
39	chr14:39638000-39639000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
40	chr14:39638000-39639000	Active TSS	Brain Germinal Matrix	brain
41	chr14:39638000-39639200	Flanking Active TSS	Primary T cells from cord blood	blood
42	chr14:39638000-39639400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
43	chr14:39638000-39640000	Active TSS	Colonic Mucosa	Colon
44	chr14:39638000-39640200	Active TSS	HUES64 Cell Line	embryonic stem cell
45	chr14:39638000-39640200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr14:39638000-39640200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr14:39638000-39640200	Active TSS	Right Ventricle	heart
48	chr14:39638000-39640400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
49	chr14:39638200-39638800	Flanking Active TSS	Thymus	Thymus
50	chr14:39638200-39639000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--

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