Variant report

Variant	rs7986690
Chromosome Location	chr13:50204331-50204332
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:50198466..50201359-chr13:50202667..50205096,2	MCF-7	breast:

Extended variants
information (count: 10 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs4941653	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7140087	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7320206	0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1047311	chr13:49895019-50224227	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	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
6	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
7	esv2752657	chr13:50144995-50244150	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription 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	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs7986690	CYSLTR2	cis	cerebellum	SCAN
rs7986690	RCBTB1	cis	cerebellum	SCAN
rs7986690	ARL11	cis	parietal	SCAN
rs7986690	RCBTB1	cis	parietal	SCAN
rs7986690	ARL11	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:50200400-50209800	Weak transcription	Gastric	stomach
2	chr13:50202000-50204600	Flanking Active TSS	Primary B cells from cord blood	blood
3	chr13:50202000-50204600	Enhancers	Fetal Heart	heart
4	chr13:50202000-50205200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr13:50202400-50210000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr13:50202800-50204600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr13:50202800-50204600	Enhancers	HepG2	liver
8	chr13:50202800-50205000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr13:50202800-50233600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr13:50203000-50204400	Weak transcription	Esophagus	oesophagus
11	chr13:50203000-50204400	Weak transcription	Fetal Intestine Small	intestine
12	chr13:50203000-50204600	Enhancers	Skeletal Muscle Female	skeletal muscle
13	chr13:50203000-50205000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
14	chr13:50203000-50209000	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr13:50203000-50209000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
16	chr13:50203000-50209400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
17	chr13:50203200-50204400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
18	chr13:50203200-50204400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr13:50203200-50204400	Weak transcription	Fetal Muscle Trunk	muscle
20	chr13:50203200-50204600	Weak transcription	Thymus	Thymus
21	chr13:50203200-50204600	Enhancers	K562	blood
22	chr13:50203200-50204800	Enhancers	Placenta	Placenta
23	chr13:50203200-50208800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr13:50203200-50209000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr13:50203200-50210600	Weak transcription	Small Intestine	intestine
26	chr13:50203200-50212200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr13:50203400-50204600	Weak transcription	Lung	lung
28	chr13:50203400-50204600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
29	chr13:50203400-50205000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr13:50203400-50209200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr13:50203600-50204400	Flanking Active TSS	GM12878-XiMat	blood
32	chr13:50203600-50204400	Enhancers	NH-A	brain
33	chr13:50203600-50204800	Enhancers	Left Ventricle	heart
34	chr13:50203600-50209800	Weak transcription	Primary T cells from cord blood	blood
35	chr13:50203800-50204600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr13:50203800-50204600	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells short term culture	blood
37	chr13:50204000-50204400	Genic enhancers	Primary B cells from peripheral blood	blood
38	chr13:50204000-50204400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr13:50204000-50204400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr13:50204000-50204600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr13:50204000-50205000	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr13:50204000-50209200	Weak transcription	HUES6 Cell Line	embryonic stem cell
43	chr13:50204000-50209200	Weak transcription	Right Atrium	heart
44	chr13:50204000-50209800	Weak transcription	Rectal Mucosa Donor 29	rectum
45	chr13:50204200-50204400	Enhancers	Primary monocytes fromperipheralblood	blood
46	chr13:50204200-50204400	Enhancers	Duodenum Smooth Muscle	Duodenum
47	chr13:50204200-50204400	Enhancers	HUVEC	blood vessel
48	chr13:50204200-50204800	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr13:50204200-50204800	Weak transcription	Fetal Thymus	thymus
50	chr13:50204200-50205000	Genic enhancers	Primary hematopoietic stem cells	blood

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