Variant report

Variant	rs3782930
Chromosome Location	chr13:50317222-50317223
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:50316640..50318955-chr13:50509690..50511603,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000123178	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs12585586	0.80[ASN][1000 genomes]
rs2146437	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2897771	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6561563	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7338721	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7982132	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9526596	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9526599	0.80[AFR][1000 genomes]
rs9535304	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9535308	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9535313	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9535319	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535321	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535328	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535334	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9535335	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9562919	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9568313	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9568317	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9568330	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9596183	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9596186	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9596187	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	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
4	nsv900074	chr13:50317104-50381016	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs3782930	EBPL	cis	Artery Tibial	GTEx
rs3782930	KPNA3	Cis_1M	lymphoblastoid	RTeQTL
rs3782930	EBPL	cis	lung	GTEx
rs3782930	EBPL	cis	Whole Blood	GTEx
rs3782930	EBPL	Cis_1M	lymphoblastoid	RTeQTL
rs3782930	EBPL	cis	Esophagus Muscularis	GTEx
rs3782930	EBPL	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:50266400-50349000	Weak transcription	Esophagus	oesophagus
2	chr13:50273200-50326000	Weak transcription	Aorta	Aorta
3	chr13:50273200-50333800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr13:50277000-50318400	Weak transcription	Hela-S3	cervix
5	chr13:50290000-50324000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr13:50290000-50334000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr13:50293200-50326000	Weak transcription	Fetal Brain Male	brain
8	chr13:50294200-50324000	Weak transcription	Rectal Smooth Muscle	rectum
9	chr13:50294400-50333000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr13:50296200-50330400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr13:50296400-50320200	Weak transcription	Spleen	Spleen
12	chr13:50296600-50330400	Weak transcription	Small Intestine	intestine
13	chr13:50296600-50338600	Weak transcription	Ovary	ovary
14	chr13:50297000-50322400	Weak transcription	Brain Cingulate Gyrus	brain
15	chr13:50298000-50327600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr13:50299200-50327600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr13:50299400-50319400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr13:50300600-50345600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr13:50300800-50321800	Weak transcription	Brain Anterior Caudate	brain
20	chr13:50301000-50319200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr13:50301200-50323600	Weak transcription	Colon Smooth Muscle	Colon
22	chr13:50301200-50327800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr13:50302800-50333800	Weak transcription	Thymus	Thymus
24	chr13:50303200-50319400	Weak transcription	Primary neutrophils fromperipheralblood	blood
25	chr13:50303200-50334000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr13:50304400-50321400	Weak transcription	Duodenum Mucosa	Duodenum
27	chr13:50305600-50319400	Weak transcription	Fetal Intestine Small	intestine
28	chr13:50305600-50319600	Weak transcription	Fetal Stomach	stomach
29	chr13:50305800-50319400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr13:50305800-50320200	Weak transcription	Fetal Muscle Leg	muscle
31	chr13:50306000-50318400	Weak transcription	Placenta	Placenta
32	chr13:50306000-50319000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr13:50306000-50320200	Weak transcription	Stomach Smooth Muscle	stomach
34	chr13:50306000-50324000	Weak transcription	HSMMtube	muscle
35	chr13:50306000-50351600	Weak transcription	Rectal Mucosa Donor 29	rectum
36	chr13:50306200-50323200	Weak transcription	Brain Germinal Matrix	brain
37	chr13:50306200-50334200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr13:50306200-50336200	Weak transcription	Adipose Nuclei	Adipose
39	chr13:50306600-50318200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
40	chr13:50306600-50319000	Weak transcription	Osteobl	bone
41	chr13:50306600-50323200	Weak transcription	NHEK	skin
42	chr13:50306800-50317800	Weak transcription	Primary monocytes fromperipheralblood	blood
43	chr13:50306800-50318000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
44	chr13:50306800-50318000	Weak transcription	HUVEC	blood vessel
45	chr13:50306800-50319000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr13:50306800-50333800	Weak transcription	H1 Cell Line	embryonic stem cell
47	chr13:50307200-50318200	Weak transcription	HUES48 Cell Line	embryonic stem cell
48	chr13:50307200-50318200	Weak transcription	HUES64 Cell Line	embryonic stem cell
49	chr13:50307400-50317400	Weak transcription	Cortex derived primary cultured neurospheres	brain
50	chr13:50308000-50318800	Weak transcription	Primary T helper cells PMA-I stimulated	--

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