Variant report

Variant	rs2295791
Chromosome Location	chr6:38084569-38084570
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10456458	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12194275	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.95[MEX][hapmap];0.98[MKK][hapmap];0.93[TSI][hapmap];0.90[YRI][hapmap];0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12206414	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12214320	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12661200	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13196716	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1967149	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2201645	0.83[EUR][1000 genomes]
rs2645117	0.81[CHB][hapmap];0.88[GIH][hapmap];0.95[MEX][hapmap];0.87[TSI][hapmap]
rs2645124	0.80[CEU][hapmap]
rs2842505	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4541739	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4711523	0.91[CHB][hapmap];0.83[CHD][hapmap];0.80[JPT][hapmap]
rs4714117	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4714120	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]
rs6458041	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6925864	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][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	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
7	nsv885817	chr6:38036420-39019503	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
8	nsv534620	chr6:38049585-38602064	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2295791	MDGA1	cis	cerebellum	SCAN
rs2295791	KCNK17	cis	parietal	SCAN

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:38030800-38085800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
2	chr6:38045600-38107000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr6:38053000-38090400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr6:38057200-38109200	Weak transcription	K562	blood
5	chr6:38059800-38091600	Weak transcription	Spleen	Spleen
6	chr6:38060000-38092000	Weak transcription	Aorta	Aorta
7	chr6:38060000-38099400	Weak transcription	Right Ventricle	heart
8	chr6:38060000-38108200	Weak transcription	Ovary	ovary
9	chr6:38063400-38085600	Weak transcription	A549	lung
10	chr6:38063800-38099000	Weak transcription	NH-A	brain
11	chr6:38071800-38091400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr6:38072000-38085400	Weak transcription	GM12878-XiMat	blood
13	chr6:38072200-38108400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr6:38074200-38086000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr6:38074600-38085800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr6:38074600-38086000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
17	chr6:38075200-38092000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr6:38075200-38118200	Weak transcription	Colonic Mucosa	Colon
19	chr6:38075400-38103800	Weak transcription	Pancreas	Pancrea
20	chr6:38076400-38091400	Strong transcription	Primary B cells from cord blood	blood
21	chr6:38076600-38085600	Weak transcription	Gastric	stomach
22	chr6:38076600-38104000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr6:38078800-38084600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr6:38078800-38085600	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr6:38078800-38086000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr6:38078800-38086400	Weak transcription	Brain Substantia Nigra	brain
27	chr6:38078800-38086600	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr6:38078800-38087400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr6:38078800-38099000	Weak transcription	NHDF-Ad	bronchial
30	chr6:38078800-38109000	Weak transcription	Rectal Smooth Muscle	rectum
31	chr6:38078800-38111000	Weak transcription	Fetal Kidney	kidney
32	chr6:38078800-38111000	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr6:38079000-38086000	Weak transcription	Brain Cingulate Gyrus	brain
34	chr6:38079400-38085400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr6:38079600-38113800	Weak transcription	Placenta Amnion	Placenta Amnion
36	chr6:38079800-38086200	Weak transcription	Brain Hippocampus Middle	brain
37	chr6:38079800-38088600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr6:38080400-38085600	Weak transcription	HUES6 Cell Line	embryonic stem cell
39	chr6:38080400-38086600	Weak transcription	HUES64 Cell Line	embryonic stem cell
40	chr6:38080400-38104800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr6:38081400-38087000	Weak transcription	Fetal Brain Female	brain
42	chr6:38081600-38084600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr6:38081800-38084800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr6:38081800-38121800	Weak transcription	Psoas Muscle	Psoas
45	chr6:38082200-38085200	Enhancers	HMEC	breast
46	chr6:38082200-38086400	Weak transcription	Brain Anterior Caudate	brain
47	chr6:38082400-38086000	Weak transcription	H9 Cell Line	embryonic stem cell
48	chr6:38082400-38086800	Weak transcription	Brain Germinal Matrix	brain
49	chr6:38082400-38087200	Weak transcription	Fetal Brain Male	brain
50	chr6:38082600-38094400	Weak transcription	H1 Cell Line	embryonic stem cell

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