Variant report

Variant	rs10821312
Chromosome Location	chr9:96944581-96944582
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:96943921..96946821-chr9:96947982..96950934,2	MCF-7	breast:
2	chr9:96858833..96861735-chr9:96944084..96946628,2	K562	blood:
3	chr9:96942774..96945747-chr9:96959750..96962534,2	K562	blood:
4	chr9:96762359..96764035-chr9:96943994..96946319,2	K562	blood:
5	chr9:96927843..96930054-chr9:96943540..96946724,4	MCF-7	breast:
6	chr9:96940341..96943331-chr9:96943637..96946113,2	MCF-7	breast:
7	chr9:96934105..96937234-chr9:96943114..96945589,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000199133	Chromatin interaction
ENSG00000269946	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10115278	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10116369	0.81[MKK][hapmap]
rs10117272	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10117305	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10122644	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10512232	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10821307	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10821315	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10993093	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12342389	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12345620	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12377837	1.00[CHB][hapmap]
rs12378444	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2080658	1.00[CHB][hapmap]
rs4744321	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.86[MEX][hapmap];1.00[MKK][hapmap];0.90[TSI][hapmap];0.89[YRI][hapmap];0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4744324	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4744326	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6479530	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67631527	0.86[ASN][1000 genomes]
rs7025626	1.00[CHB][hapmap]
rs7038156	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7865658	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8115	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	nsv482457	chr9:96813852-96996170	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	217 gene(s)	inside rSNPs	diseases
2	nsv831655	chr9:96834042-97042009	Enhancers Weak transcription Genic enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	218 gene(s)	inside rSNPs	diseases
3	esv3394266	chr9:96935210-97045514	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	195 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10821312	SLC35D2	cis	cerebellum	SCAN

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:96929800-96944800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr9:96929800-96948400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr9:96931400-96965600	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr9:96936800-96945200	Weak transcription	Fetal Intestine Small	intestine
5	chr9:96937200-96944800	Weak transcription	Fetal Heart	heart
6	chr9:96937200-96959400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr9:96937800-96946600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr9:96938200-96949000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr9:96938400-96944600	Strong transcription	HSMMtube	muscle
10	chr9:96938400-96947400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr9:96939400-96945000	Weak transcription	Colonic Mucosa	Colon
12	chr9:96939400-96948400	Weak transcription	Brain Germinal Matrix	brain
13	chr9:96939600-96944800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr9:96939600-96944800	Weak transcription	Brain Substantia Nigra	brain
15	chr9:96939600-96945000	Weak transcription	Gastric	stomach
16	chr9:96939600-96945400	Weak transcription	Stomach Smooth Muscle	stomach
17	chr9:96939600-96947200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr9:96939600-96947600	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr9:96939600-96948000	Weak transcription	Fetal Brain Female	brain
20	chr9:96939600-96949400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr9:96939600-96950600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
22	chr9:96939800-96944600	Weak transcription	Hela-S3	cervix
23	chr9:96939800-96944800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr9:96939800-96944800	Weak transcription	Right Ventricle	heart
25	chr9:96939800-96945000	Weak transcription	NHLF	lung
26	chr9:96939800-96945200	Weak transcription	Pancreas	Pancrea
27	chr9:96939800-96945400	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr9:96939800-96946800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr9:96939800-96946800	Strong transcription	Muscle Satellite Cultured Cells	--
30	chr9:96939800-96947200	Weak transcription	Esophagus	oesophagus
31	chr9:96939800-96947400	Strong transcription	Osteobl	bone
32	chr9:96939800-96948400	Weak transcription	Rectal Mucosa Donor 31	rectum
33	chr9:96939800-96960800	Weak transcription	NHDF-Ad	bronchial
34	chr9:96940000-96944600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
35	chr9:96940000-96946800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr9:96940000-96949200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
37	chr9:96940400-96945000	Weak transcription	Rectal Mucosa Donor 29	rectum
38	chr9:96940400-96945600	Weak transcription	Primary T helper cells fromperipheralblood	blood
39	chr9:96940400-96947800	Weak transcription	Duodenum Mucosa	Duodenum
40	chr9:96940400-96955600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr9:96940600-96945000	Weak transcription	Fetal Intestine Large	intestine
42	chr9:96940600-96945200	Weak transcription	Small Intestine	intestine
43	chr9:96940600-96947200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
44	chr9:96940800-96950400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr9:96941000-96945800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
46	chr9:96941200-96944800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr9:96941200-96946800	Strong transcription	Fetal Muscle Trunk	muscle
48	chr9:96941400-96944800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr9:96941400-96959400	Weak transcription	Spleen	Spleen
50	chr9:96941600-96947600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood

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