Variant report

Variant	rs9349322
Chromosome Location	chr6:45634092-45634093
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:45617993..45619581-chr6:45633411..45635573,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RUNX2-2	chr6:45634067-45634483	XLOC_005303

Extended variants
information (count: 31 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs12175323	0.91[ASN][1000 genomes]
rs12661654	0.91[CHB][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs12663985	0.95[CHB][hapmap];0.86[JPT][hapmap];0.92[ASN][1000 genomes]
rs12665728	0.91[ASN][1000 genomes]
rs1388242	0.81[JPT][hapmap]
rs1388244	0.81[JPT][hapmap]
rs1491144	0.81[ASN][1000 genomes]
rs1932040	0.81[CEU][hapmap]
rs1994682	0.95[CHB][hapmap];0.86[JPT][hapmap];0.92[ASN][1000 genomes]
rs2035791	0.81[ASN][1000 genomes]
rs2396505	0.81[JPT][hapmap]
rs321325	0.81[JPT][hapmap]
rs4326224	0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs4714863	0.86[ASN][1000 genomes]
rs6458457	0.91[ASN][1000 genomes]
rs7752609	0.85[ASN][1000 genomes]
rs7761790	0.88[ASN][1000 genomes]
rs7762915	0.95[CHB][hapmap];0.85[JPT][hapmap];0.88[ASN][1000 genomes]
rs7769966	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7774097	0.89[ASN][1000 genomes]
rs9349323	0.86[ASN][1000 genomes]
rs9369569	0.85[ASN][1000 genomes]
rs9395112	0.81[TSI][hapmap]
rs9472541	1.00[CHB][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs9472547	0.92[ASN][1000 genomes]
rs9472548	0.91[ASN][1000 genomes]
rs9472552	0.81[JPT][hapmap]
rs9472557	0.81[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1028393	chr6:44875558-45822335	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv538211	chr6:44875558-45822335	ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
3	nsv532024	chr6:45475088-45982640	Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9349322	ABCC10	cis	cerebellum	SCAN
rs9349322	CAPN11	cis	parietal	SCAN

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:45630400-45635000	Weak transcription	NHDF-Ad	bronchial
2	chr6:45631000-45634200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
3	chr6:45631000-45635600	Enhancers	NH-A	brain
4	chr6:45631800-45634200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
5	chr6:45631800-45635000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr6:45631800-45635400	Weak transcription	Esophagus	oesophagus
7	chr6:45631800-45645000	Weak transcription	Colonic Mucosa	Colon
8	chr6:45632000-45634600	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr6:45632000-45635000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr6:45632000-45635000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr6:45632000-45635200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr6:45632000-45643400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr6:45632200-45634800	Weak transcription	NHLF	lung
14	chr6:45632200-45636600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr6:45632400-45635200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr6:45632600-45635600	Strong transcription	HSMM	muscle
17	chr6:45632600-45643400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr6:45632800-45634200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
19	chr6:45633000-45634800	Enhancers	ES-I3 Cell Line	embryonic stem cell
20	chr6:45633200-45634200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr6:45633200-45634200	Enhancers	Primary T helper cells PMA-I stimulated	--
22	chr6:45633200-45634200	Enhancers	Primary T helper cells fromperipheralblood	blood
23	chr6:45633200-45634200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr6:45633200-45635200	Enhancers	iPS-18 Cell Line	embryonic stem cell
25	chr6:45633200-45635400	Enhancers	HUES6 Cell Line	embryonic stem cell
26	chr6:45633200-45635400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr6:45633200-45635800	Enhancers	Primary hematopoietic stem cells short term culture	blood
28	chr6:45633400-45634200	Enhancers	Primary T cells fromperipheralblood	blood
29	chr6:45633400-45635200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr6:45633400-45635400	Enhancers	Primary B cells from peripheral blood	blood
31	chr6:45633400-45635600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr6:45633600-45634200	Enhancers	HUES64 Cell Line	embryonic stem cell
33	chr6:45633600-45634200	Enhancers	Fetal Thymus	thymus
34	chr6:45633600-45635000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr6:45633800-45634200	Enhancers	HUES48 Cell Line	embryonic stem cell
36	chr6:45633800-45634400	Enhancers	H1 Cell Line	embryonic stem cell
37	chr6:45633800-45634400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr6:45633800-45634600	Enhancers	iPS-20b Cell Line	embryonic stem cell
39	chr6:45633800-45635200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr6:45634000-45634200	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
41	chr6:45634000-45635000	Weak transcription	Primary hematopoietic stem cells	blood

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