Variant report

Variant	rs2734
Chromosome Location	chr13:52367207-52367208
allele	A/G
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	RCOR1	chr13:52367037-52367396	K562	blood:	n/a	n/a
2	USF2	chr13:52367155-52367220	GM12878	blood:	n/a	n/a
3	JUN	chr13:52367073-52368457	K562	blood:	n/a	chr13:52367658-52367665 chr13:52367832-52367842 chr13:52367658-52367666 chr13:52367832-52367842 chr13:52367832-52367842 chr13:52367823-52367830 chr13:52367822-52367830 chr13:52367822-52367830 chr13:52368161-52368170 chr13:52367658-52367666 chr13:52367832-52367842 chr13:52368446-52368455

No.	Distal block	Cell Line	Cell type
1	chr13:52024232..52029374-chr13:52366504..52381003,28	MCF-7	breast:
2	chr13:52361705..52366550-chr13:52366781..52371643,5	MCF-7	breast:
3	chr13:52363946..52366197-chr13:52367048..52368673,2	K562	blood:

Variant related genes	Relation type
DHRS12	TF binding region
ENSG00000102786	Chromatin interaction
ENSG00000224892	Chromatin interaction
ENSG00000236778	Chromatin interaction
ENSG00000102796	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs2760302	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2760303	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2760304	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[TSI][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2760305	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2773267	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.95[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2773268	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2773269	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.95[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs512948	1.00[CEU][hapmap];0.88[GIH][hapmap];0.83[TSI][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs518210	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs541434	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs732004	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9535761	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530718	chr13:52291802-52832752	Enhancers ZNF genes & repeats Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv933424	chr13:52293482-52507732	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv455884	chr13:52302630-52405251	Enhancers Flanking Active TSS Strong transcription Genic enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
4	nsv561644	chr13:52302630-52405251	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
5	nsv455887	chr13:52318522-52405251	Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
6	nsv561645	chr13:52318522-52405251	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
7	nsv1044310	chr13:52321564-52643924	Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
8	nsv1050117	chr13:52325116-52643924	Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
9	esv1840020	chr13:52345838-52388765	Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
10	nsv934070	chr13:52362588-53174923	Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Active TSS Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2734	FNDC3A	cis	cerebellum	SCAN

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:52339600-52375000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
2	chr13:52339800-52371400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr13:52339800-52375200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr13:52344600-52371800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
5	chr13:52346400-52376000	Weak transcription	Thymus	Thymus
6	chr13:52348200-52375600	Weak transcription	Primary T helper cells fromperipheralblood	blood
7	chr13:52348200-52375600	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr13:52353000-52368200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr13:52355000-52370600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr13:52356000-52371000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr13:52356000-52371400	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr13:52356200-52367600	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr13:52356400-52367600	Weak transcription	Primary B cells from cord blood	blood
14	chr13:52356600-52367600	Weak transcription	Primary B cells from peripheral blood	blood
15	chr13:52357200-52371200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr13:52358000-52372000	Weak transcription	HepG2	liver
17	chr13:52358600-52368200	Weak transcription	Fetal Intestine Small	intestine
18	chr13:52358600-52375600	Weak transcription	Colonic Mucosa	Colon
19	chr13:52359000-52375600	Weak transcription	Rectal Mucosa Donor 29	rectum
20	chr13:52360400-52373600	Weak transcription	HUES64 Cell Line	embryonic stem cell
21	chr13:52360600-52376000	Weak transcription	Gastric	stomach
22	chr13:52360800-52370600	Weak transcription	Aorta	Aorta
23	chr13:52360800-52371000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr13:52360800-52375600	Weak transcription	Fetal Intestine Large	intestine
25	chr13:52361000-52374800	Weak transcription	Stomach Mucosa	stomach
26	chr13:52361000-52375600	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr13:52361200-52367800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
28	chr13:52361400-52367400	Weak transcription	HSMMtube	muscle
29	chr13:52361400-52373200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr13:52361600-52367400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr13:52361600-52367800	Weak transcription	Fetal Stomach	stomach
32	chr13:52361600-52368000	Weak transcription	Spleen	Spleen
33	chr13:52361600-52370000	Weak transcription	Fetal Heart	heart
34	chr13:52361600-52370000	Weak transcription	Placenta	Placenta
35	chr13:52361600-52370200	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr13:52361600-52370400	Weak transcription	Skeletal Muscle Female	skeletal muscle
37	chr13:52361600-52371600	Weak transcription	Brain Angular Gyrus	brain
38	chr13:52361600-52372200	Weak transcription	Rectal Mucosa Donor 31	rectum
39	chr13:52361600-52374400	Weak transcription	Colon Smooth Muscle	Colon
40	chr13:52361600-52374400	Weak transcription	Pancreatic Islets	Pancreatic Islet
41	chr13:52361600-52374600	Weak transcription	Brain Cingulate Gyrus	brain
42	chr13:52361600-52374600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr13:52361600-52375000	Weak transcription	Duodenum Mucosa	Duodenum
44	chr13:52361600-52375800	Weak transcription	Brain Germinal Matrix	brain
45	chr13:52361600-52376400	Weak transcription	Fetal Brain Female	brain
46	chr13:52361800-52367600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
47	chr13:52361800-52368600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr13:52361800-52369000	Weak transcription	Skeletal Muscle Male	skeletal muscle
49	chr13:52361800-52369200	Weak transcription	Lung	lung
50	chr13:52361800-52370400	Weak transcription	Right Ventricle	heart

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