Variant report

Variant	rs343500
Chromosome Location	chr9:6015011-6015012
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:6006778..6010531-chr9:6011866..6018012,11	MCF-7	breast:

Variant related genes	Relation type
ENSG00000183354	Chromatin interaction
ENSG00000263575	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10121480	1.00[CEU][hapmap]
rs10733517	1.00[CEU][hapmap];1.00[TSI][hapmap]
rs10733518	0.90[EUR][1000 genomes]
rs10733520	1.00[CEU][hapmap]
rs10733522	0.82[AFR][1000 genomes]
rs10733523	0.85[AFR][1000 genomes]
rs10739079	1.00[CEU][hapmap]
rs10758731	1.00[CEU][hapmap]
rs10758732	1.00[CEU][hapmap]
rs10758734	1.00[CEU][hapmap];1.00[TSI][hapmap]
rs10815330	1.00[CEU][hapmap]
rs10815335	1.00[CEU][hapmap];1.00[TSI][hapmap]
rs1331378	1.00[CEU][hapmap];0.81[YRI][hapmap]
rs1331379	1.00[CEU][hapmap]
rs1418740	1.00[CEU][hapmap]
rs1478935	0.83[AFR][1000 genomes]
rs1478936	0.81[AFR][1000 genomes]
rs1478938	0.84[GIH][hapmap]
rs16923578	1.00[CEU][hapmap]
rs1776008	1.00[TSI][hapmap]
rs186913	1.00[CEU][hapmap]
rs2045959	0.90[ASN][1000 genomes]
rs2150703	1.00[CEU][hapmap];1.00[TSI][hapmap]
rs2244053	1.00[CEU][hapmap]
rs2244058	1.00[CEU][hapmap]
rs2291055	1.00[CEU][hapmap];0.83[YRI][hapmap]
rs2381360	1.00[CEU][hapmap]
rs2773340	0.82[AFR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2773341	1.00[EUR][1000 genomes]
rs343469	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap]
rs343471	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]
rs343480	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs343482	1.00[CEU][hapmap];0.88[JPT][hapmap];1.00[EUR][1000 genomes]
rs343483	1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3739649	1.00[CEU][hapmap];1.00[TSI][hapmap]
rs404267	1.00[EUR][1000 genomes]
rs4075225	1.00[CEU][hapmap]
rs419595	0.90[EUR][1000 genomes]
rs4265236	1.00[CEU][hapmap]
rs4389996	1.00[CEU][hapmap]
rs4395943	1.00[CEU][hapmap];0.94[GIH][hapmap];1.00[TSI][hapmap]
rs459718	0.90[EUR][1000 genomes]
rs460564	1.00[EUR][1000 genomes]
rs4740833	1.00[CEU][hapmap]
rs4742131	1.00[CEU][hapmap];1.00[TSI][hapmap]
rs6477017	1.00[CEU][hapmap]
rs6477024	1.00[CEU][hapmap];0.83[YRI][hapmap];0.85[AFR][1000 genomes]
rs6477025	0.85[AFR][1000 genomes]
rs6477026	0.83[AFR][1000 genomes]
rs7019606	1.00[CEU][hapmap]
rs7021498	1.00[CEU][hapmap]
rs7024130	1.00[CEU][hapmap];0.94[GIH][hapmap];1.00[TSI][hapmap]
rs7029833	1.00[CEU][hapmap]
rs7030731	1.00[CEU][hapmap];0.83[YRI][hapmap]
rs7032130	1.00[CEU][hapmap]
rs7034210	1.00[CEU][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes]
rs7037680	1.00[TSI][hapmap]
rs7042947	1.00[CEU][hapmap];0.86[JPT][hapmap];0.90[EUR][1000 genomes]
rs7044750	1.00[CEU][hapmap]
rs7846916	1.00[EUR][1000 genomes]
rs7851749	0.85[AFR][1000 genomes]
rs7866793	1.00[CEU][hapmap]
rs7868062	1.00[CEU][hapmap]
rs7869571	0.82[AFR][1000 genomes]
rs7875450	0.85[AFR][1000 genomes]
rs899381	0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948847	chr9:5712626-6417677	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv1031086	chr9:5806949-6630686	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
3	nsv539967	chr9:5806949-6630686	Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
4	nsv892155	chr9:5825768-6044937	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
5	nsv1015450	chr9:5915640-6114652	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs343500	SCGB2A2	trans	brain	seeQTL
rs343500	SCGB1D2	trans	brain	seeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:6008600-6015200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr9:6014200-6015200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr9:6014200-6015200	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
4	chr9:6014200-6015200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
5	chr9:6014200-6016200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr9:6014200-6016400	Active TSS	ES-I3 Cell Line	embryonic stem cell
7	chr9:6014400-6015200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
8	chr9:6014400-6015200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
9	chr9:6014400-6015200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
10	chr9:6014400-6015200	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
11	chr9:6014400-6015200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr9:6014400-6015200	Flanking Active TSS	Brain Anterior Caudate	brain
13	chr9:6014400-6015200	Flanking Active TSS	Brain Cingulate Gyrus	brain
14	chr9:6014400-6015200	Flanking Active TSS	Brain Substantia Nigra	brain
15	chr9:6014400-6015200	Flanking Active TSS	Duodenum Mucosa	Duodenum
16	chr9:6014400-6015200	Flanking Active TSS	Fetal Heart	heart
17	chr9:6014400-6015200	Flanking Active TSS	Stomach Smooth Muscle	stomach
18	chr9:6014400-6015200	Enhancers	Spleen	Spleen
19	chr9:6014400-6015200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
20	chr9:6014400-6015200	Flanking Active TSS	Osteobl	bone
21	chr9:6014400-6015400	Flanking Active TSS	Primary B cells from cord blood	blood
22	chr9:6014400-6015400	Flanking Active TSS	Primary hematopoietic stem cells	blood
23	chr9:6014400-6015400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
24	chr9:6014400-6015400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr9:6014400-6015400	Flanking Active TSS	Adipose Nuclei	Adipose
26	chr9:6014400-6015400	Flanking Active TSS	HUVEC	blood vessel
27	chr9:6014400-6015600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
28	chr9:6014400-6016000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr9:6014400-6016400	Active TSS	iPS-20b Cell Line	embryonic stem cell
30	chr9:6014600-6015200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
31	chr9:6014600-6015200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
32	chr9:6014600-6015200	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
33	chr9:6014600-6015200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
34	chr9:6014600-6015200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr9:6014600-6015200	Flanking Active TSS	Liver	Liver
36	chr9:6014600-6015200	Flanking Active TSS	Brain Angular Gyrus	brain
37	chr9:6014600-6015200	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
38	chr9:6014600-6015200	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
39	chr9:6014600-6015200	Flanking Active TSS	Fetal Lung	lung
40	chr9:6014600-6015200	Flanking Active TSS	Fetal Muscle Leg	muscle
41	chr9:6014600-6015200	Flanking Active TSS	Fetal Thymus	thymus
42	chr9:6014600-6015200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
43	chr9:6014600-6015200	Flanking Active TSS	Dnd41	blood
44	chr9:6014600-6015200	Flanking Active TSS	NHEK	skin
45	chr9:6014600-6015400	Flanking Active TSS	Primary T cells from cord blood	blood
46	chr9:6014600-6016000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr9:6014600-6016000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr9:6014600-6016200	Active TSS	H9 Cell Line	embryonic stem cell
49	chr9:6014600-6016200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr9:6014600-6016200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung

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