Variant report

Variant	rs1206196
Chromosome Location	chr11:64897453-64897454
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:64897351..64905868-chr11:64946257..64954528,24	K562	blood:
2	chr11:64779689..64782801-chr11:64896069..64898995,3	MCF-7	breast:
3	chr11:64877522..64908330-chr11:64931619..64960265,171	MCF-7	breast:
4	chr11:64896045..64898859-chr11:64925808..64928234,2	MCF-7	breast:
5	chr11:64894864..64904857-chr11:64934599..64944069,37	K562	blood:
6	chr11:64894025..64897642-chr11:64945042..64952225,7	MCF-7	breast:

Variant related genes	Relation type
ENSG00000014216	Chromatin interaction
ENSG00000273003	Chromatin interaction
ENSG00000254614	Chromatin interaction
ENSG00000255058	Chromatin interaction
ENSG00000255200	Chromatin interaction
ENSG00000213465	Chromatin interaction
ENSG00000204710	Chromatin interaction
ENSG00000249251	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs11227123	0.82[YRI][hapmap]
rs1129195	0.82[CEU][hapmap]
rs1152639	0.96[CEU][hapmap];0.87[GIH][hapmap];1.00[MEX][hapmap]
rs1196043	0.94[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.98[TSI][hapmap];0.89[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1196045	0.96[CEU][hapmap];0.89[GIH][hapmap];0.95[MEX][hapmap]
rs12362669	1.00[JPT][hapmap];0.88[YRI][hapmap];0.86[ASN][1000 genomes]
rs12363102	0.87[ASN][1000 genomes]
rs1706937	0.94[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2282499	0.82[CEU][hapmap]
rs35661464	0.87[ASN][1000 genomes]
rs3850946	0.85[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.87[ASN][1000 genomes]
rs3850947	0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.89[ASN][1000 genomes]
rs4258384	0.87[ASN][1000 genomes]
rs544944	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs769440	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv526181	chr11:64638041-65257329	Flanking Active TSS Enhancers Strong transcription Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1539 gene(s)	inside rSNPs	diseases
2	nsv897711	chr11:64772545-64900270	Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	109 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs1206196	RAB1B	cis	parietal	SCAN
rs1206196	FADS1	cis	parietal	SCAN
rs1206196	NCBP2	trans	parietal	SCAN
rs1206196	SCGB1D4	cis	parietal	SCAN
rs1206196	FADS3	cis	cerebellum	SCAN
rs1206196	SNORD31	cis	parietal	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:64890200-64900600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr11:64890200-64900800	Weak transcription	Right Atrium	heart
3	chr11:64890800-64899200	Weak transcription	Fetal Brain Male	brain
4	chr11:64891000-64899600	Strong transcription	Placenta	Placenta
5	chr11:64891000-64900200	Weak transcription	Fetal Heart	heart
6	chr11:64891200-64900000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr11:64891200-64900200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr11:64891400-64900000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr11:64891600-64898400	Strong transcription	Skeletal Muscle Male	skeletal muscle
10	chr11:64891600-64898800	Strong transcription	Rectal Mucosa Donor 29	rectum
11	chr11:64891600-64899400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr11:64891600-64899800	Strong transcription	Primary T cells from cord blood	blood
13	chr11:64891600-64899800	Strong transcription	Fetal Stomach	stomach
14	chr11:64891600-64899800	Strong transcription	Fetal Thymus	thymus
15	chr11:64891600-64900400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr11:64891600-64900400	Strong transcription	HUES48 Cell Line	embryonic stem cell
17	chr11:64891800-64897600	Strong transcription	Liver	Liver
18	chr11:64891800-64898200	Strong transcription	Fetal Muscle Trunk	muscle
19	chr11:64891800-64898800	Strong transcription	Primary T cells fromperipheralblood	blood
20	chr11:64891800-64899000	Strong transcription	Primary T helper cells fromperipheralblood	blood
21	chr11:64891800-64899000	Strong transcription	Dnd41	blood
22	chr11:64891800-64899200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr11:64891800-64899200	Strong transcription	Brain Cingulate Gyrus	brain
24	chr11:64891800-64899400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
25	chr11:64891800-64899400	Strong transcription	Fetal Muscle Leg	muscle
26	chr11:64891800-64899400	Strong transcription	Stomach Smooth Muscle	stomach
27	chr11:64891800-64899600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
28	chr11:64891800-64899600	Strong transcription	Primary T helper naive cells from peripheral blood	blood
29	chr11:64891800-64899600	Strong transcription	Fetal Brain Female	brain
30	chr11:64891800-64899800	Strong transcription	HUES64 Cell Line	embryonic stem cell
31	chr11:64891800-64899800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
32	chr11:64891800-64899800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr11:64891800-64899800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr11:64891800-64899800	Strong transcription	Fetal Intestine Large	intestine
35	chr11:64891800-64900000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr11:64891800-64900000	Strong transcription	Fetal Intestine Small	intestine
37	chr11:64891800-64900200	Strong transcription	H9 Cell Line	embryonic stem cell
38	chr11:64891800-64900200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr11:64891800-64900200	Strong transcription	Muscle Satellite Cultured Cells	--
40	chr11:64891800-64900200	Strong transcription	Brain Anterior Caudate	brain
41	chr11:64891800-64900200	Strong transcription	Brain Hippocampus Middle	brain
42	chr11:64891800-64900200	Strong transcription	Placenta Amnion	Placenta Amnion
43	chr11:64891800-64900200	Strong transcription	NHLF	lung
44	chr11:64891800-64900200	Strong transcription	Osteobl	bone
45	chr11:64891800-64900400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr11:64891800-64900400	Strong transcription	HUES6 Cell Line	embryonic stem cell
47	chr11:64891800-64900400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr11:64891800-64900400	Strong transcription	Cortex derived primary cultured neurospheres	brain
49	chr11:64891800-64900400	Strong transcription	Ovary	ovary
50	chr11:64891800-64900400	Strong transcription	Thymus	Thymus

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