Variant report

Variant	rs4714738
Chromosome Location	chr6:44056585-44056586
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:44040495..44042700-chr6:44055821..44057827,2	K562	blood:
2	chr6:43738183..43740736-chr6:44055058..44057255,2	K562	blood:
3	chr6:44055370..44058215-chr6:44094927..44096529,2	K562	blood:
4	chr6:44055374..44057616-chr6:44223363..44225359,2	MCF-7	breast:
5	chr6:44055370..44058215-chr6:44094460..44096529,3	K562	blood:
6	chr6:43738183..43740736-chr6:44054818..44057255,3	K562	blood:
7	chr6:44050029..44051784-chr6:44053653..44056587,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000237686	Chromatin interaction
ENSG00000112715	Chromatin interaction
ENSG00000157593	Chromatin interaction
ENSG00000231881	Chromatin interaction
ENSG00000137216	Chromatin interaction
ENSG00000272114	Chromatin interaction
ENSG00000180992	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10948121	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12191873	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12202501	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs12206795	1.00[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs2064639	1.00[AFR][1000 genomes]
rs2064640	1.00[AFR][1000 genomes]
rs2092870	1.00[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs2236061	1.00[AFR][1000 genomes]
rs3734695	0.87[JPT][hapmap]
rs3734697	1.00[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs4628095	1.00[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs4711764	1.00[ASW][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs4711766	1.00[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs4714750	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs4714754	1.00[ASW][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs4714759	1.00[ASW][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs4714761	1.00[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];0.87[JPT][hapmap];0.85[ASN][1000 genomes]
rs4714762	0.83[ASN][1000 genomes]
rs62401766	1.00[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs62403189	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs729391	1.00[ASW][hapmap]
rs833805	1.00[ASW][hapmap]
rs877112	0.94[JPT][hapmap]
rs9349270	1.00[AFR][1000 genomes]
rs9349271	1.00[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs9349272	0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs9349275	1.00[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs9357432	1.00[ASW][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.93[JPT][hapmap];1.00[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs9369448	0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs9369449	1.00[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs9369450	1.00[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs9369453	1.00[ASW][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs9369454	1.00[ASW][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs9369456	0.86[ASN][1000 genomes]
rs9369457	1.00[AFR][1000 genomes]
rs9369458	0.87[JPT][hapmap]
rs9381287	1.00[AFR][1000 genomes]
rs9381294	1.00[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs9394984	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931987	chr6:43624625-44350167	Enhancers Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	201 gene(s)	inside rSNPs	diseases
2	nsv462935	chr6:44046143-44117607	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	nsv603002	chr6:44046143-44117607	Genic enhancers Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv981140	chr6:44055862-44060195	Weak transcription Genic enhancers Enhancers Strong transcription ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs4714738	GPR116	cis	parietal	SCAN
rs4714738	CNPY3	cis	cerebellum	SCAN
rs4714738	TMEM63B	cis	cerebellum	SCAN
rs4714738	MRPL14	cis	cerebellum	SCAN
rs4714738	MRPS10	cis	parietal	SCAN

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:44044200-44067000	Weak transcription	NHDF-Ad	bronchial
2	chr6:44044600-44067600	Weak transcription	Spleen	Spleen
3	chr6:44044800-44062200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr6:44044800-44067000	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr6:44044800-44067400	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr6:44044800-44070200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr6:44044800-44071400	Weak transcription	Colon Smooth Muscle	Colon
8	chr6:44045000-44067400	Weak transcription	Brain Anterior Caudate	brain
9	chr6:44045000-44071800	Weak transcription	Aorta	Aorta
10	chr6:44045600-44067000	Weak transcription	Fetal Brain Female	brain
11	chr6:44046200-44057000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr6:44047000-44066600	Weak transcription	Thymus	Thymus
13	chr6:44047200-44056800	Weak transcription	Brain Hippocampus Middle	brain
14	chr6:44047200-44057000	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr6:44047400-44056800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr6:44047400-44059000	Weak transcription	Fetal Brain Male	brain
17	chr6:44047400-44061600	Weak transcription	Stomach Smooth Muscle	stomach
18	chr6:44047400-44061800	Weak transcription	Brain Angular Gyrus	brain
19	chr6:44047400-44062000	Weak transcription	Brain Germinal Matrix	brain
20	chr6:44047400-44062000	Weak transcription	Rectal Mucosa Donor 29	rectum
21	chr6:44047400-44067200	Weak transcription	Dnd41	blood
22	chr6:44047400-44067400	Weak transcription	Primary B cells from peripheral blood	blood
23	chr6:44047400-44067600	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr6:44047400-44069200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr6:44047400-44071400	Weak transcription	Primary T helper cells PMA-I stimulated	--
26	chr6:44048800-44060800	Weak transcription	NHLF	lung
27	chr6:44049200-44062000	Weak transcription	Ovary	ovary
28	chr6:44049400-44061800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr6:44049400-44061800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr6:44049400-44067000	Weak transcription	GM12878-XiMat	blood
31	chr6:44049800-44061800	Weak transcription	Fetal Thymus	thymus
32	chr6:44051600-44067400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr6:44052600-44067000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr6:44052600-44071000	Weak transcription	HSMMtube	muscle
35	chr6:44052800-44057000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr6:44052800-44061600	Weak transcription	HUES48 Cell Line	embryonic stem cell
37	chr6:44052800-44067000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
38	chr6:44052800-44067400	Weak transcription	HUES6 Cell Line	embryonic stem cell
39	chr6:44052800-44071000	Weak transcription	Placenta	Placenta
40	chr6:44052800-44071800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr6:44053000-44067000	Weak transcription	H1 Cell Line	embryonic stem cell
42	chr6:44053000-44067000	Weak transcription	HUES64 Cell Line	embryonic stem cell
43	chr6:44053000-44070400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr6:44053200-44056600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr6:44053200-44061600	Weak transcription	NHEK	skin
46	chr6:44053400-44057000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr6:44054000-44056600	Weak transcription	K562	blood
48	chr6:44054600-44056600	Weak transcription	Primary T cells from cord blood	blood
49	chr6:44054800-44067400	Weak transcription	Primary hematopoietic stem cells	blood
50	chr6:44055000-44061600	Weak transcription	Adipose Nuclei	Adipose

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