Variant report

Variant	rs17301365
Chromosome Location	chr3:136662529-136662530
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FAM48A	chr3:136662484-136662552	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:136660169..136663903-chr3:136675087..136677294,3	K562	blood:
2	chr3:136656593..136659304-chr3:136661529..136663519,2	MCF-7	breast:
3	chr3:136658510..136660043-chr3:136661343..136664014,2	MCF-7	breast:

Variant related genes	Relation type
IL20RB	TF binding region
NCK1	TF binding region
ENSG00000174564	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs1048145	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17366890	1.00[ASN][1000 genomes]
rs56308712	0.82[AFR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59361983	0.82[EUR][1000 genomes]
rs6439655	1.00[CHB][hapmap]
rs67546863	0.82[EUR][1000 genomes]
rs67923745	0.82[EUR][1000 genomes]
rs73230077	0.82[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs73230078	0.82[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs73230095	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73231917	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs73231937	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73231943	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73231944	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73231953	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73231958	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73231966	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73231974	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73231975	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[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	nsv877531	chr3:136517016-136662954	Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
2	nsv877532	chr3:136526939-136662603	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
3	nsv877533	chr3:136539689-136662954	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs17301365	TMEM22	cis	cerebellum	SCAN
rs17301365	VCAN	trans	cerebellum	SCAN
rs17301365	STAG1	cis	cerebellum	SCAN
rs17301365	ATP1B3	cis	cerebellum	SCAN

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:136624200-136664400	Weak transcription	Aorta	Aorta
2	chr3:136638800-136664400	Weak transcription	Duodenum Mucosa	Duodenum
3	chr3:136639000-136664400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr3:136641000-136670000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr3:136645400-136664200	Weak transcription	Placenta	Placenta
6	chr3:136645800-136664600	Weak transcription	Fetal Muscle Trunk	muscle
7	chr3:136646200-136664400	Weak transcription	Ovary	ovary
8	chr3:136646600-136673800	Weak transcription	Pancreas	Pancrea
9	chr3:136647600-136664400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr3:136648600-136673800	Weak transcription	Fetal Intestine Small	intestine
11	chr3:136650200-136666600	Weak transcription	Brain Angular Gyrus	brain
12	chr3:136650200-136669400	Weak transcription	Colonic Mucosa	Colon
13	chr3:136650800-136664400	Weak transcription	Stomach Smooth Muscle	stomach
14	chr3:136652400-136664600	Weak transcription	Primary B cells from peripheral blood	blood
15	chr3:136654000-136664400	Weak transcription	Fetal Stomach	stomach
16	chr3:136655600-136664400	Weak transcription	Primary hematopoietic stem cells	blood
17	chr3:136655600-136664600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr3:136655600-136664600	Weak transcription	Fetal Kidney	kidney
19	chr3:136655800-136664400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr3:136656000-136664400	Weak transcription	Fetal Intestine Large	intestine
21	chr3:136656200-136662800	Enhancers	Primary T helper cells fromperipheralblood	blood
22	chr3:136656400-136664400	Weak transcription	Primary B cells from cord blood	blood
23	chr3:136656400-136664400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr3:136656400-136664600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr3:136656400-136664600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
26	chr3:136656400-136681400	Weak transcription	Fetal Muscle Leg	muscle
27	chr3:136656600-136662800	Enhancers	Primary T helper cells PMA-I stimulated	--
28	chr3:136657200-136664400	Weak transcription	HSMMtube	muscle
29	chr3:136657400-136664400	Weak transcription	K562	blood
30	chr3:136657400-136673200	Weak transcription	NH-A	brain
31	chr3:136657600-136664600	Weak transcription	Fetal Lung	lung
32	chr3:136657800-136664400	Weak transcription	Primary neutrophils fromperipheralblood	blood
33	chr3:136657800-136664600	Weak transcription	HSMM	muscle
34	chr3:136658200-136671200	Weak transcription	Muscle Satellite Cultured Cells	--
35	chr3:136658400-136666000	Weak transcription	HepG2	liver
36	chr3:136658600-136679400	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr3:136659000-136664400	Weak transcription	Gastric	stomach
38	chr3:136659200-136664400	Weak transcription	Rectal Mucosa Donor 31	rectum
39	chr3:136659400-136664600	Weak transcription	Hela-S3	cervix
40	chr3:136660200-136663000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
41	chr3:136660200-136664400	Weak transcription	Fetal Heart	heart
42	chr3:136660200-136664400	Weak transcription	GM12878-XiMat	blood
43	chr3:136661000-136662600	Enhancers	ES-I3 Cell Line	embryonic stem cell
44	chr3:136661000-136662600	Enhancers	HUES6 Cell Line	embryonic stem cell
45	chr3:136661000-136662600	Enhancers	HUES64 Cell Line	embryonic stem cell
46	chr3:136661000-136662600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
47	chr3:136661000-136662600	Enhancers	NHEK	skin
48	chr3:136661000-136662800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
49	chr3:136661000-136662800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr3:136661200-136662600	Enhancers	iPS-20b Cell Line	embryonic stem cell

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