Variant report

Variant	rs3796373
Chromosome Location	chr3:45960851-45960852
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	POLR2A	chr3:45960807-45962617	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:45957988..45959492-chr3:45959750..45961379,2	K562	blood:

Variant related genes	Relation type
LZTFL1	TF binding region

Extended variants
information (count: 41 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs1072755	0.91[CHB][hapmap];0.93[CHD][hapmap];0.90[ASN][1000 genomes]
rs13066048	0.82[CHB][hapmap];0.84[ASN][1000 genomes]
rs13091821	0.82[ASN][1000 genomes]
rs13091979	0.82[ASN][1000 genomes]
rs1532071	0.84[ASN][1000 genomes]
rs1552489	0.86[CHB][hapmap];0.90[CHD][hapmap];0.84[ASN][1000 genomes]
rs1552490	0.84[ASN][1000 genomes]
rs1601867	0.82[ASN][1000 genomes]
rs17078449	0.81[CHD][hapmap]
rs1994488	0.84[ASN][1000 genomes]
rs1994489	0.84[ASN][1000 genomes]
rs2054866	0.82[CHB][hapmap];0.90[CHD][hapmap];0.82[ASN][1000 genomes]
rs2171530	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2234358	0.82[CHB][hapmap];0.93[CHD][hapmap];0.82[ASN][1000 genomes]
rs2248228	0.91[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs2291470	0.99[ASN][1000 genomes]
rs35465473	0.82[ASN][1000 genomes]
rs3733103	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs3774634	0.85[CHB][hapmap];0.82[ASN][1000 genomes]
rs3774635	0.82[ASN][1000 genomes]
rs3774639	0.82[CHB][hapmap];0.90[CHD][hapmap];0.84[ASN][1000 genomes]
rs4535265	0.86[CHB][hapmap];0.93[CHD][hapmap];0.85[ASN][1000 genomes]
rs4682799	0.86[CHB][hapmap];0.93[CHD][hapmap];0.84[ASN][1000 genomes]
rs4682800	0.84[CHB][hapmap];0.84[ASN][1000 genomes]
rs4683148	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs4683149	0.93[ASN][1000 genomes]
rs4683152	0.89[ASN][1000 genomes]
rs4683154	0.84[ASN][1000 genomes]
rs4683156	0.82[ASN][1000 genomes]
rs6800954	0.82[CHB][hapmap];0.86[CHD][hapmap];0.81[MEX][hapmap]
rs7129	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs7623476	0.82[CEU][hapmap]
rs9311380	0.84[ASN][1000 genomes]
rs936938	0.86[CHB][hapmap];0.87[ASN][1000 genomes]
rs936939	0.81[CHD][hapmap]
rs9824253	0.83[ASN][1000 genomes]
rs9831315	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876734	chr3:45725031-46468467	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv498008	chr3:45733423-46319401	Strong transcription Active TSS Genic enhancers Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv834678	chr3:45804294-46010256	Enhancers Flanking Bivalent TSS/Enh Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	nsv876736	chr3:45900621-46027410	Strong transcription Enhancers Transcr. at gene 5' and 3' Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3796373	SHISA5	cis	parietal	SCAN

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:45943000-45961000	Weak transcription	Brain Substantia Nigra	brain
2	chr3:45943600-45961200	Weak transcription	Gastric	stomach
3	chr3:45948200-45961000	Weak transcription	Rectal Smooth Muscle	rectum
4	chr3:45948400-45961600	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr3:45949200-45962400	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr3:45949800-45962600	Weak transcription	HepG2	liver
7	chr3:45952800-45963600	Weak transcription	Psoas Muscle	Psoas
8	chr3:45952800-45964600	Weak transcription	Fetal Heart	heart
9	chr3:45956800-45961800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr3:45957400-45961600	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr3:45957400-45963000	Weak transcription	Colon Smooth Muscle	Colon
12	chr3:45957600-45965000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr3:45957800-45961200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr3:45957800-45961400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr3:45957800-45962400	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr3:45957800-45962600	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr3:45957800-45962600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr3:45957800-45962600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr3:45957800-45963000	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr3:45957800-45963000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr3:45957800-45963600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr3:45957800-45963600	Weak transcription	Colonic Mucosa	Colon
23	chr3:45957800-45969000	Weak transcription	K562	blood
24	chr3:45957800-45971200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr3:45958000-45961000	Weak transcription	Rectal Mucosa Donor 29	rectum
26	chr3:45958000-45961400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr3:45958000-45961400	Weak transcription	HSMMtube	muscle
28	chr3:45958000-45962400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
29	chr3:45958000-45962800	Weak transcription	Brain Germinal Matrix	brain
30	chr3:45958000-45964400	Weak transcription	Stomach Mucosa	stomach
31	chr3:45958000-45964600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr3:45958000-45964800	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr3:45958000-45965000	Weak transcription	Osteobl	bone
34	chr3:45958000-45965200	Weak transcription	HSMM	muscle
35	chr3:45958000-45969000	Weak transcription	NH-A	brain
36	chr3:45958000-45980800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr3:45958200-45961200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
38	chr3:45958200-45961600	Weak transcription	Primary B cells from peripheral blood	blood
39	chr3:45958200-45963200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
40	chr3:45958200-45963400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
41	chr3:45958400-45963000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
42	chr3:45958400-45966200	Strong transcription	Stomach Smooth Muscle	stomach
43	chr3:45958400-45974200	Strong transcription	Fetal Stomach	stomach
44	chr3:45958600-45962000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
45	chr3:45958600-45963000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
46	chr3:45958600-45968800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
47	chr3:45958600-45970000	Weak transcription	Small Intestine	intestine
48	chr3:45958800-45962600	Weak transcription	HUES64 Cell Line	embryonic stem cell
49	chr3:45958800-45964600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr3:45958800-45980000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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