Variant report

Variant	rs4714120
Chromosome Location	chr6:37999223-37999224
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:37786371..37788627-chr6:37999131..38001315,2	MCF-7	breast:
2	chr6:37991053..37993262-chr6:37997611..38000343,2	K562	blood:

Variant related genes	Relation type
ENSG00000156639	Chromatin interaction
ENSG00000225945	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10456458	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs10485029	0.82[MEX][hapmap];0.87[TSI][hapmap]
rs1187421	0.81[CHB][hapmap];0.85[TSI][hapmap]
rs12190570	0.81[CHB][hapmap]
rs12194275	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.93[TSI][hapmap];0.81[EUR][1000 genomes]
rs12206414	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12214320	0.81[EUR][1000 genomes]
rs12661200	0.81[EUR][1000 genomes]
rs13196716	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs1967149	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2201645	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2295791	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes]
rs259679	0.81[CHB][hapmap]
rs259718	0.81[CHB][hapmap]
rs2645117	0.81[CHB][hapmap];0.83[GIH][hapmap];0.82[MEX][hapmap];0.87[TSI][hapmap]
rs2842505	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4541739	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4711523	0.91[CHB][hapmap];0.83[CHD][hapmap];0.82[GIH][hapmap];0.80[JPT][hapmap];0.88[ASN][1000 genomes]
rs4714117	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6458041	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs6909195	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6925864	0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1028825	chr6:37495154-38278320	Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv1017051	chr6:37789341-38084719	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv538203	chr6:37789341-38084719	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv1020625	chr6:37833591-38155622	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
5	nsv1021991	chr6:37893949-38738720	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
6	esv34450	chr6:37963308-38007241	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	esv2763549	chr6:37985025-38014006	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
8	esv2754649	chr6:37985025-38147910	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4714120	MDGA1	cis	cerebellum	SCAN
rs4714120	KCNK17	cis	parietal	SCAN

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:37985000-38002400	Weak transcription	Primary B cells from cord blood	blood
2	chr6:37985000-38030200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr6:37985200-38001400	Weak transcription	Small Intestine	intestine
4	chr6:37988000-38001400	Weak transcription	Stomach Mucosa	stomach
5	chr6:37990400-38000400	Weak transcription	Brain Hippocampus Middle	brain
6	chr6:37990600-38005800	Weak transcription	Stomach Smooth Muscle	stomach
7	chr6:37993000-38001800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr6:37994400-38011400	Weak transcription	Aorta	Aorta
9	chr6:37995200-38000800	Weak transcription	Primary T helper cells fromperipheralblood	blood
10	chr6:37995600-38001200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr6:37995800-38001200	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr6:37995800-38003800	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr6:37995800-38005400	Weak transcription	Psoas Muscle	Psoas
14	chr6:37995800-38008000	Weak transcription	Fetal Muscle Leg	muscle
15	chr6:37995800-38013000	Weak transcription	Fetal Thymus	thymus
16	chr6:37995800-38020600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr6:37996000-38000200	Weak transcription	Brain Anterior Caudate	brain
18	chr6:37996000-38000200	Weak transcription	Colon Smooth Muscle	Colon
19	chr6:37996000-38000400	Weak transcription	Brain Angular Gyrus	brain
20	chr6:37996000-38000800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
21	chr6:37996000-38001200	Weak transcription	Brain Substantia Nigra	brain
22	chr6:37996000-38001200	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr6:37996000-38001200	Weak transcription	Rectal Smooth Muscle	rectum
24	chr6:37996000-38001400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
25	chr6:37996000-38002000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
26	chr6:37996000-38002600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr6:37996000-38015400	Weak transcription	HSMMtube	muscle
28	chr6:37996200-38005400	Weak transcription	Brain Cingulate Gyrus	brain
29	chr6:37996200-38008000	Weak transcription	Monocytes-CD14+_RO01746	blood
30	chr6:37996200-38008600	Weak transcription	HUVEC	blood vessel
31	chr6:37996400-38000400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr6:37996400-38001400	Weak transcription	Primary T cells from cord blood	blood
33	chr6:37996600-38001200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
34	chr6:37996600-38002000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr6:37996600-38002000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr6:37996600-38002400	Weak transcription	NHDF-Ad	bronchial
37	chr6:37996800-38000400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr6:37997000-38000200	Weak transcription	Pancreatic Islets	Pancreatic Islet
39	chr6:37997000-38001800	Weak transcription	Adipose Nuclei	Adipose
40	chr6:37997000-38002400	Weak transcription	Primary hematopoietic stem cells	blood
41	chr6:37997200-38001200	Weak transcription	Liver	Liver
42	chr6:37997200-38001800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr6:37997200-38002400	Weak transcription	Muscle Satellite Cultured Cells	--
44	chr6:37997200-38002800	Weak transcription	Osteobl	bone
45	chr6:37997400-38000200	Weak transcription	Primary T helper cells PMA-I stimulated	--
46	chr6:37997600-38002400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr6:37997600-38007000	Weak transcription	A549	lung
48	chr6:37997800-38002000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr6:37998400-37999400	Enhancers	iPS-18 Cell Line	embryonic stem cell
50	chr6:37998400-38000200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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