Variant report

Variant	rs11789439
Chromosome Location	chr9:101820718-101820719
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:101819756..101821876-chr9:101984546..101986258,2	K562	blood:
2	chr9:101820521..101822703-chr9:101866221..101868544,2	MCF-7	breast:
3	chr9:101778237..101780848-chr9:101819627..101821830,2	K562	blood:
4	chr9:101819637..101822232-chr9:101894406..101896072,2	K562	blood:
5	chr9:101797638..101801423-chr9:101817658..101821818,3	K562	blood:

Variant related genes	Relation type
ENSG00000106803	Chromatin interaction
ENSG00000106799	Chromatin interaction
ENSG00000204291	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs11788317	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs16918167	0.89[ASW][hapmap];0.94[CEU][hapmap];0.80[LWK][hapmap];0.95[MEX][hapmap];0.89[MKK][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3780617	1.00[CEU][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3780620	0.95[MEX][hapmap]
rs4480177	0.86[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs7030799	0.88[CEU][hapmap];0.90[JPT][hapmap]
rs7031588	0.82[ASW][hapmap];0.83[CEU][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs7038068	1.00[CEU][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7047475	0.88[CEU][hapmap];0.90[JPT][hapmap]
rs7874819	0.88[CEU][hapmap];0.82[MEX][hapmap]
rs869776	0.88[CEU][hapmap];0.82[MEX][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv893618	chr9:101800106-101886071	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11789439	C9orf30	cis	parietal	SCAN
rs11789439	TSTD2	cis	parietal	SCAN
rs11789439	COL15A1	cis	lymphoblastoid	seeQTL
rs11789439	HIATL1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:101793800-101837600	Weak transcription	Psoas Muscle	Psoas
2	chr9:101807000-101831800	Strong transcription	Fetal Muscle Trunk	muscle
3	chr9:101807600-101831800	Strong transcription	Fetal Muscle Leg	muscle
4	chr9:101809200-101821600	Weak transcription	Brain Anterior Caudate	brain
5	chr9:101813200-101833000	Weak transcription	Lung	lung
6	chr9:101813600-101825600	Weak transcription	Aorta	Aorta
7	chr9:101814200-101826600	Weak transcription	Fetal Intestine Large	intestine
8	chr9:101814200-101829400	Weak transcription	Fetal Intestine Small	intestine
9	chr9:101815600-101821400	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr9:101816200-101844200	Weak transcription	Gastric	stomach
11	chr9:101816800-101821200	Enhancers	HMEC	breast
12	chr9:101816800-101822400	Enhancers	Osteobl	bone
13	chr9:101817000-101821600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr9:101817600-101821000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr9:101818000-101834800	Weak transcription	Pancreas	Pancrea
16	chr9:101818800-101823600	Enhancers	Primary monocytes fromperipheralblood	blood
17	chr9:101818800-101829000	Weak transcription	Ovary	ovary
18	chr9:101819000-101820800	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
19	chr9:101819000-101821600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
20	chr9:101819000-101822000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr9:101819200-101821600	Enhancers	NHDF-Ad	bronchial
22	chr9:101819200-101822400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr9:101819200-101822400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
24	chr9:101819400-101821000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
25	chr9:101819400-101821200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr9:101819400-101821400	Genic enhancers	Adipose Nuclei	Adipose
27	chr9:101819400-101821800	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr9:101819400-101821800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr9:101819400-101822000	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
30	chr9:101819400-101822200	Enhancers	NHLF	lung
31	chr9:101819400-101822400	Enhancers	Spleen	Spleen
32	chr9:101819600-101821000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
33	chr9:101819600-101821000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
34	chr9:101819600-101822200	Flanking Active TSS	Primary B cells from cord blood	blood
35	chr9:101819600-101822200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
36	chr9:101819600-101822200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr9:101819800-101820800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr9:101819800-101820800	Enhancers	Liver	Liver
39	chr9:101819800-101820800	Active TSS	Rectal Mucosa Donor 29	rectum
40	chr9:101819800-101820800	Flanking Active TSS	HSMM	muscle
41	chr9:101819800-101820800	Flanking Active TSS	NH-A	brain
42	chr9:101819800-101821000	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
43	chr9:101819800-101821000	Flanking Active TSS	GM12878-XiMat	blood
44	chr9:101819800-101821000	Flanking Active TSS	K562	blood
45	chr9:101819800-101821200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
46	chr9:101819800-101821200	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
47	chr9:101819800-101821200	Genic enhancers	HSMMtube	muscle
48	chr9:101819800-101821600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr9:101819800-101821800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
50	chr9:101819800-101821800	Genic enhancers	Rectal Smooth Muscle	rectum

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