Variant report

Variant	rs6901565
Chromosome Location	chr6:24836161-24836162
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 13 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10498721	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.93[MEX][hapmap];0.85[MKK][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10946731	0.93[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.98[LWK][hapmap];0.88[MKK][hapmap];0.85[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4513786	0.85[CEU][hapmap];1.00[CHB][hapmap];0.93[GIH][hapmap];0.85[TSI][hapmap];0.86[EUR][1000 genomes]
rs4583980	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4712856	0.85[CEU][hapmap];1.00[CHB][hapmap];0.94[GIH][hapmap];0.88[TSI][hapmap];0.86[EUR][1000 genomes]
rs7741582	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7741583	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9358804	0.94[GIH][hapmap];0.88[TSI][hapmap];0.85[EUR][1000 genomes]
rs9467322	0.83[CEU][hapmap];0.82[AMR][1000 genomes];0.80[EUR][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	nsv830609	chr6:24712086-24896647	Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
2	nsv1022966	chr6:24763776-25154212	Flanking Active TSS Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv538160	chr6:24763776-25154212	Active TSS Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
4	nsv508396	chr6:24779648-24846309	Weak transcription Enhancers Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6901565	C6orf62	cis	cerebellum	SCAN
rs6901565	HIST1H1T	cis	cerebellum	SCAN
rs6901565	FLJ32130	trans	multi-tissue	Pritchard
rs6901565	KIAA0319	cis	cerebellum	SCAN

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:24777000-24847600	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr6:24777000-24859600	Weak transcription	Psoas Muscle	Psoas
3	chr6:24788800-24848200	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr6:24789200-24842600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
5	chr6:24798200-24841200	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr6:24800000-24843200	Weak transcription	Liver	Liver
7	chr6:24804800-24858200	Weak transcription	Gastric	stomach
8	chr6:24806200-24842400	Weak transcription	Rectal Smooth Muscle	rectum
9	chr6:24808800-24845600	Weak transcription	Fetal Stomach	stomach
10	chr6:24809800-24839200	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr6:24817800-24839600	Strong transcription	Primary T cells from cord blood	blood
12	chr6:24817800-24840800	Strong transcription	Primary B cells from peripheral blood	blood
13	chr6:24817800-24854400	Strong transcription	Primary B cells from cord blood	blood
14	chr6:24817800-24855800	Strong transcription	Primary neutrophils fromperipheralblood	blood
15	chr6:24818000-24836200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr6:24818000-24840000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
17	chr6:24818000-24840600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr6:24818000-24840600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr6:24818600-24855800	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr6:24818800-24856000	Strong transcription	Primary monocytes fromperipheralblood	blood
21	chr6:24818800-24856400	Strong transcription	Monocytes-CD14+_RO01746	blood
22	chr6:24822400-24840200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr6:24822600-24844000	Weak transcription	Fetal Heart	heart
24	chr6:24827400-24836200	Strong transcription	Thymus	Thymus
25	chr6:24827600-24836200	Strong transcription	HSMMtube	muscle
26	chr6:24827800-24840800	Weak transcription	Lung	lung
27	chr6:24828000-24840600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr6:24828000-24842600	Weak transcription	Dnd41	blood
29	chr6:24828400-24840600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr6:24829800-24836200	Strong transcription	Fetal Thymus	thymus
31	chr6:24830400-24855800	Weak transcription	Stomach Smooth Muscle	stomach
32	chr6:24831000-24841200	Enhancers	Breast Myoepithelial Primary Cells	Breast
33	chr6:24831200-24837200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr6:24832200-24839200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr6:24832400-24836200	Enhancers	Brain Anterior Caudate	brain
36	chr6:24832400-24859600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr6:24832800-24838200	Weak transcription	Placenta Amnion	Placenta Amnion
38	chr6:24833000-24838200	Weak transcription	Placenta	Placenta
39	chr6:24833000-24838400	Weak transcription	Aorta	Aorta
40	chr6:24833000-24839400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr6:24833000-24857800	Weak transcription	Brain Angular Gyrus	brain
42	chr6:24833200-24836200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr6:24833200-24845400	Weak transcription	NHDF-Ad	bronchial
44	chr6:24833400-24838400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr6:24833400-24840400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
46	chr6:24833400-24841000	Weak transcription	Skeletal Muscle Male	skeletal muscle
47	chr6:24834000-24836800	Genic enhancers	Primary T helper cells PMA-I stimulated	--
48	chr6:24834600-24844400	Weak transcription	Brain Hippocampus Middle	brain
49	chr6:24834600-24851600	Weak transcription	HSMM	muscle
50	chr6:24834800-24836400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--

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