Variant report

Variant	rs10733517
Chromosome Location	chr9:5883409-5883410
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:5828344..5834722-chr9:5880387..5886482,7	MCF-7	breast:
2	chr9:5839459..5843654-chr9:5878363..5884455,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000099219	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10121480	1.00[CEU][hapmap]
rs10733518	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10733520	1.00[CEU][hapmap]
rs10739079	1.00[CEU][hapmap]
rs10758713	1.00[LWK][hapmap]
rs10758731	1.00[CEU][hapmap]
rs10758732	1.00[CEU][hapmap]
rs10758734	1.00[CEU][hapmap];1.00[TSI][hapmap]
rs10815301	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10815302	1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10815330	1.00[CEU][hapmap]
rs10815335	1.00[CEU][hapmap];1.00[TSI][hapmap]
rs1260130	1.00[TSI][hapmap]
rs1331378	1.00[CEU][hapmap]
rs1331379	1.00[CEU][hapmap]
rs1418740	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16923551	1.00[ASW][hapmap]
rs16923578	1.00[CEU][hapmap]
rs1776008	1.00[TSI][hapmap]
rs186913	1.00[CEU][hapmap]
rs2150703	1.00[CEU][hapmap];0.87[GIH][hapmap];1.00[TSI][hapmap]
rs2225469	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2244053	1.00[CEU][hapmap]
rs2244058	1.00[CEU][hapmap]
rs2291055	1.00[CEU][hapmap]
rs2381360	1.00[CEU][hapmap]
rs2797512	1.00[TSI][hapmap]
rs2797519	1.00[TSI][hapmap]
rs343469	1.00[CEU][hapmap]
rs343471	1.00[CEU][hapmap];1.00[TSI][hapmap]
rs343480	1.00[CEU][hapmap]
rs343482	1.00[CEU][hapmap]
rs343500	1.00[CEU][hapmap];1.00[TSI][hapmap]
rs3739649	1.00[CEU][hapmap];1.00[TSI][hapmap]
rs4075225	1.00[CEU][hapmap]
rs4265236	1.00[CEU][hapmap]
rs4389996	1.00[CEU][hapmap]
rs4395943	1.00[CEU][hapmap];1.00[TSI][hapmap]
rs4740833	1.00[CEU][hapmap]
rs4742131	1.00[ASW][hapmap];1.00[CEU][hapmap];0.87[GIH][hapmap];1.00[TSI][hapmap]
rs6477017	1.00[CEU][hapmap]
rs6477024	1.00[CEU][hapmap]
rs7019606	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7021498	1.00[CEU][hapmap]
rs7024130	1.00[CEU][hapmap];1.00[TSI][hapmap]
rs7029833	1.00[CEU][hapmap]
rs7030731	1.00[CEU][hapmap]
rs7032130	1.00[CEU][hapmap]
rs7034210	1.00[CEU][hapmap];0.86[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7037680	1.00[TSI][hapmap]
rs7039787	0.90[EUR][1000 genomes]
rs7042947	1.00[CEU][hapmap];0.86[JPT][hapmap];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7044750	1.00[CEU][hapmap]
rs7846916	0.80[ASN][1000 genomes]
rs7866793	1.00[CEU][hapmap]
rs7868062	1.00[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1017103	chr9:5509431-5987907	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv539965	chr9:5509431-5987907	ZNF genes & repeats Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	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
4	esv3331803	chr9:5766129-5905103	Weak transcription Enhancers Bivalent/Poised TSS Genic enhancers Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
5	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
6	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
7	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
8	nsv1033546	chr9:5875201-5900427	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	esv3322610	chr9:5883334-5883672	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10733517	KCNB2	trans	brain	seeQTL
rs10733517	SCGB1D2	trans	brain	seeQTL
rs10733517	SCGB2A2	trans	brain	seeQTL

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:5834400-5886000	Weak transcription	Brain Cingulate Gyrus	brain
2	chr9:5840400-5921600	Weak transcription	Right Ventricle	heart
3	chr9:5852200-5897000	Weak transcription	Primary T helper cells fromperipheralblood	blood
4	chr9:5853800-5895600	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr9:5854400-5886200	Weak transcription	Brain Anterior Caudate	brain
6	chr9:5856800-5895600	Weak transcription	Brain Substantia Nigra	brain
7	chr9:5858600-5885800	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr9:5859000-5895600	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr9:5859000-5906600	Weak transcription	Ovary	ovary
10	chr9:5859200-5919800	Weak transcription	Fetal Brain Female	brain
11	chr9:5863400-5895600	Weak transcription	Fetal Intestine Small	intestine
12	chr9:5863600-5896600	Weak transcription	Pancreas	Pancrea
13	chr9:5864800-5895600	Weak transcription	Gastric	stomach
14	chr9:5865200-5886000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
15	chr9:5870000-5886400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr9:5870800-5895600	Weak transcription	Stomach Smooth Muscle	stomach
17	chr9:5871000-5895600	Weak transcription	Brain Hippocampus Middle	brain
18	chr9:5871000-5920000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr9:5871200-5898400	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr9:5875600-5884800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr9:5876000-5885000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr9:5876800-5886000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr9:5877000-5895600	Weak transcription	Left Ventricle	heart
24	chr9:5877000-5896000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr9:5877200-5886200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr9:5877200-5886200	Weak transcription	Brain Angular Gyrus	brain
27	chr9:5877200-5894200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
28	chr9:5877200-5895400	Weak transcription	Fetal Stomach	stomach
29	chr9:5877200-5895600	Weak transcription	Aorta	Aorta
30	chr9:5880000-5886000	Weak transcription	A549	lung
31	chr9:5880200-5884400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr9:5880400-5883800	Weak transcription	NHEK	skin
33	chr9:5880400-5884200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr9:5880600-5883800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr9:5880600-5884000	Weak transcription	HMEC	breast
36	chr9:5880600-5884400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr9:5880600-5887200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr9:5881200-5884000	Weak transcription	Hela-S3	cervix
39	chr9:5882200-5896200	Weak transcription	Spleen	Spleen
40	chr9:5882400-5886200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
41	chr9:5882400-5895400	Weak transcription	Primary T cells from cord blood	blood
42	chr9:5883000-5906400	Weak transcription	Fetal Brain Male	brain
43	chr9:5883400-5884600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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