Variant report

Variant	rs9596183
Chromosome Location	chr13:50307834-50307835
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:50264137..50266449-chr13:50305520..50308098,2	K562	blood:
2	chr13:50306515..50309235-chr13:50364713..50367239,2	K562	blood:

Variant related genes	Relation type
ENSG00000102753	Chromatin interaction
ENSG00000123179	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs12585586	0.97[ASN][1000 genomes]
rs2146437	0.82[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs2897771	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3782930	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3809325	0.90[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.81[LWK][hapmap];0.92[MEX][hapmap];0.89[MKK][hapmap];0.92[YRI][hapmap];0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6561557	0.82[ASW][hapmap];0.84[YRI][hapmap]
rs6561563	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7338721	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7982132	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7983905	0.87[ASN][1000 genomes]
rs7983918	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs9526596	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9526599	0.92[YRI][hapmap]
rs9535303	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs9535304	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9535308	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9535313	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9535319	0.84[CHB][hapmap];0.86[JPT][hapmap];0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9535321	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9535328	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9535334	1.00[CEU][hapmap];0.94[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9535335	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9535343	0.88[JPT][hapmap]
rs9562919	1.00[CEU][hapmap];0.94[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9568312	0.82[AFR][1000 genomes]
rs9568313	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9568317	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9568330	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9596186	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9596187	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[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	nsv900072	chr13:50266109-50381016	Weak transcription ZNF genes & repeats Strong transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv900073	chr13:50286218-50381016	Enhancers Active TSS Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	esv1818134	chr13:50306897-50374102	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs9596183	EBPL	cis	multi-tissue	Pritchard
rs9596183	EBPL	Cis_1M	lymphoblastoid	RTeQTL
rs9596183	EBPL	cis	lung	GTEx
rs9596183	EBPL	cis	Adipose Subcutaneous	GTEx
rs9596183	EBPL	cis	Esophagus Muscularis	GTEx
rs9596183	EBPL	cis	Whole Blood	GTEx
rs9596183	EBPL	cis	Artery Tibial	GTEx
rs9596183	KPNA3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:50266200-50316000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr13:50266400-50349000	Weak transcription	Esophagus	oesophagus
3	chr13:50273200-50326000	Weak transcription	Aorta	Aorta
4	chr13:50273200-50333800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr13:50277000-50318400	Weak transcription	Hela-S3	cervix
6	chr13:50280000-50308000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr13:50290000-50324000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr13:50290000-50334000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr13:50290200-50316800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr13:50293200-50326000	Weak transcription	Fetal Brain Male	brain
11	chr13:50294200-50315000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr13:50294200-50324000	Weak transcription	Rectal Smooth Muscle	rectum
13	chr13:50294400-50333000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr13:50294800-50314200	Weak transcription	Stomach Mucosa	stomach
15	chr13:50296200-50330400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr13:50296400-50320200	Weak transcription	Spleen	Spleen
17	chr13:50296600-50309000	Weak transcription	Brain Angular Gyrus	brain
18	chr13:50296600-50330400	Weak transcription	Small Intestine	intestine
19	chr13:50296600-50338600	Weak transcription	Ovary	ovary
20	chr13:50296800-50315000	Weak transcription	HMEC	breast
21	chr13:50297000-50322400	Weak transcription	Brain Cingulate Gyrus	brain
22	chr13:50298000-50327600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr13:50299000-50314400	Weak transcription	Fetal Brain Female	brain
24	chr13:50299200-50327600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
25	chr13:50299400-50319400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr13:50300600-50345600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr13:50300800-50321800	Weak transcription	Brain Anterior Caudate	brain
28	chr13:50301000-50319200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr13:50301200-50308400	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr13:50301200-50316000	Weak transcription	Primary B cells from peripheral blood	blood
31	chr13:50301200-50323600	Weak transcription	Colon Smooth Muscle	Colon
32	chr13:50301200-50327800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
33	chr13:50301400-50313600	Weak transcription	Rectal Mucosa Donor 31	rectum
34	chr13:50301800-50308000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr13:50302800-50333800	Weak transcription	Thymus	Thymus
36	chr13:50303200-50319400	Weak transcription	Primary neutrophils fromperipheralblood	blood
37	chr13:50303200-50334000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr13:50304000-50308000	Strong transcription	Primary T helper cells PMA-I stimulated	--
39	chr13:50304400-50316000	Weak transcription	Duodenum Smooth Muscle	Duodenum
40	chr13:50304400-50321400	Weak transcription	Duodenum Mucosa	Duodenum
41	chr13:50304600-50316000	Weak transcription	Fetal Muscle Trunk	muscle
42	chr13:50305600-50308200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr13:50305600-50308200	Enhancers	Fetal Heart	heart
44	chr13:50305600-50314600	Weak transcription	Sigmoid Colon	Sigmoid Colon
45	chr13:50305600-50319400	Weak transcription	Fetal Intestine Small	intestine
46	chr13:50305600-50319600	Weak transcription	Fetal Stomach	stomach
47	chr13:50305800-50319400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr13:50305800-50320200	Weak transcription	Fetal Muscle Leg	muscle
49	chr13:50306000-50315000	Weak transcription	Primary T cells from cord blood	blood
50	chr13:50306000-50315000	Weak transcription	Primary T cells fromperipheralblood	blood

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