Variant report

Variant	rs9535294
Chromosome Location	chr13:50246074-50246075
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:50240420..50241989-chr13:50245723..50247987,2	MCF-7	breast:
2	chr13:50243856..50246257-chr13:50421112..50423233,2	MCF-7	breast:
3	chr13:50245763..50247361-chr13:51482505..51484962,2	K562	blood:

Variant related genes	Relation type
ENSG00000136104	Chromatin interaction
ENSG00000233672	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1061979	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11148167	0.93[GIH][hapmap];0.87[MKK][hapmap];1.00[YRI][hapmap]
rs1139051	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12584401	1.00[YRI][hapmap]
rs12853861	1.00[CHD][hapmap]
rs12866447	0.93[GIH][hapmap];1.00[YRI][hapmap]
rs1923730	0.93[GIH][hapmap];0.87[MKK][hapmap];1.00[YRI][hapmap]
rs1969738	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2146142	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2236354	1.00[YRI][hapmap]
rs34480126	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4643206	1.00[YRI][hapmap]
rs4941657	1.00[YRI][hapmap]
rs4942864	0.93[GIH][hapmap];0.87[MKK][hapmap];1.00[YRI][hapmap]
rs67155750	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67394151	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67881093	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs71216551	0.93[EUR][1000 genomes]
rs7326633	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7329488	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7446	0.89[GIH][hapmap];0.87[MKK][hapmap];0.82[YRI][hapmap]
rs7991234	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7997798	0.93[GIH][hapmap];1.00[YRI][hapmap]
rs9526586	1.00[CEU][hapmap];0.82[YRI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9526588	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9535284	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535285	0.90[EUR][1000 genomes]
rs9535286	0.90[EUR][1000 genomes]
rs9535289	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535293	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9535295	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535298	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535301	0.94[CEU][hapmap];0.96[GIH][hapmap];0.88[LWK][hapmap];0.83[MKK][hapmap];0.92[TSI][hapmap];0.82[EUR][1000 genomes]
rs9535326	0.93[GIH][hapmap];0.87[MKK][hapmap];1.00[YRI][hapmap]
rs9535347	0.87[MKK][hapmap];1.00[YRI][hapmap]
rs9535352	1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916093	chr13:50050919-50290245	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv1054965	chr13:50102730-50251347	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv541771	chr13:50102730-50251347	Enhancers Active TSS Genic enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv900071	chr13:50107289-50286218	Weak transcription Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
5	nsv1043697	chr13:50129199-50249241	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
6	nsv541772	chr13:50218255-50264414	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9535294	EBPL	cis	multi-tissue	Pritchard

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:50224600-50252600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr13:50227400-50253200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr13:50231000-50246800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
4	chr13:50231800-50256000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr13:50235400-50252400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr13:50235600-50259800	Weak transcription	Right Ventricle	heart
7	chr13:50237000-50256600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
8	chr13:50237400-50256000	Weak transcription	NH-A	brain
9	chr13:50238800-50253000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr13:50240600-50253400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr13:50240800-50246400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr13:50241000-50264800	Weak transcription	Aorta	Aorta
13	chr13:50241600-50249800	Weak transcription	GM12878-XiMat	blood
14	chr13:50241800-50253400	Weak transcription	Esophagus	oesophagus
15	chr13:50241800-50256000	Weak transcription	HMEC	breast
16	chr13:50242000-50254000	Weak transcription	Fetal Brain Female	brain
17	chr13:50242200-50246200	Weak transcription	Placenta	Placenta
18	chr13:50242200-50249000	Weak transcription	NHEK	skin
19	chr13:50242200-50251200	Weak transcription	Pancreas	Pancrea
20	chr13:50242200-50251200	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr13:50242200-50251400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr13:50242200-50252000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr13:50242200-50253000	Weak transcription	Fetal Thymus	thymus
24	chr13:50242200-50253400	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr13:50242200-50256200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr13:50242200-50260600	Weak transcription	Stomach Smooth Muscle	stomach
27	chr13:50242200-50261000	Weak transcription	Duodenum Mucosa	Duodenum
28	chr13:50242200-50261400	Weak transcription	Primary T helper cells fromperipheralblood	blood
29	chr13:50242200-50264200	Weak transcription	K562	blood
30	chr13:50242200-50264400	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr13:50242200-50264400	Weak transcription	Rectal Smooth Muscle	rectum
32	chr13:50242400-50246800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr13:50242400-50246800	Weak transcription	HepG2	liver
34	chr13:50242400-50248200	Weak transcription	Colonic Mucosa	Colon
35	chr13:50242400-50248800	Weak transcription	HUES6 Cell Line	embryonic stem cell
36	chr13:50242400-50248800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr13:50242400-50248800	Weak transcription	Primary B cells from cord blood	blood
38	chr13:50242400-50249000	Weak transcription	H1 Cell Line	embryonic stem cell
39	chr13:50242400-50249000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
40	chr13:50242400-50249000	Weak transcription	Primary T cells from cord blood	blood
41	chr13:50242400-50249000	Weak transcription	Primary hematopoietic stem cells	blood
42	chr13:50242400-50249000	Weak transcription	Muscle Satellite Cultured Cells	--
43	chr13:50242400-50249000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr13:50242400-50249000	Weak transcription	Dnd41	blood
45	chr13:50242400-50249000	Weak transcription	NHLF	lung
46	chr13:50242400-50249800	Weak transcription	Primary B cells from peripheral blood	blood
47	chr13:50242400-50251000	Weak transcription	Cortex derived primary cultured neurospheres	brain
48	chr13:50242400-50251000	Weak transcription	HSMMtube	muscle
49	chr13:50242400-50251400	Weak transcription	Fetal Intestine Small	intestine
50	chr13:50242400-50252000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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