Variant report

Variant	rs928039
Chromosome Location	chr13:49554128-49554129
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	chr13:49551617..49554201-chr13:49560922..49563747,2	MCF-7	breast:
2	chr13:49552747..49554579-chr13:49576987..49579021,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CAB39L-4	chr13:49553960-49554130	ucscGeneNc_uc001vdx_2

Variant related genes	Relation type
ENSG00000201662	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs1407826	0.90[ASN][1000 genomes]
rs1937182	1.00[ASN][1000 genomes]
rs1977260	1.00[AFR][1000 genomes]
rs1983806	1.00[ASN][1000 genomes]
rs2025315	1.00[AFR][1000 genomes]
rs2181906	0.85[ASN][1000 genomes]
rs2987534	1.00[ASN][1000 genomes]
rs3012124	1.00[ASN][1000 genomes]
rs3012130	0.90[ASN][1000 genomes]
rs3012134	1.00[ASN][1000 genomes]
rs4942806	0.90[ASN][1000 genomes]
rs6561495	1.00[ASN][1000 genomes]
rs6561498	1.00[ASN][1000 genomes]
rs7326409	0.90[ASN][1000 genomes]
rs7338704	0.90[ASN][1000 genomes]
rs7999767	0.90[ASN][1000 genomes]
rs912193	0.85[ASN][1000 genomes]

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	nsv1049117	chr13:49089476-49928945	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv1034	chr13:49526761-49572727	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv455882	chr13:49531551-49679157	Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	nsv561593	chr13:49531551-49679157	Genic enhancers Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	esv1793883	chr13:49543723-49789164	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' 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
6	nsv900067	chr13:49552271-49594818	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:49548800-49554800	Active TSS	Rectal Mucosa Donor 29	rectum
2	chr13:49548800-49555800	Active TSS	Right Ventricle	heart
3	chr13:49549000-49554200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr13:49549800-49554400	Active TSS	Placenta	Placenta
5	chr13:49549800-49555000	Active TSS	Hela-S3	cervix
6	chr13:49549800-49555600	Active TSS	GM12878-XiMat	blood
7	chr13:49551000-49554800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr13:49551200-49555000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
9	chr13:49551400-49638800	Weak transcription	Pancreas	Pancrea
10	chr13:49551600-49554600	Enhancers	Primary neutrophils fromperipheralblood	blood
11	chr13:49551600-49555600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
12	chr13:49551600-49557200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
13	chr13:49551800-49554400	Enhancers	Primary T helper naive cells from peripheral blood	blood
14	chr13:49551800-49557000	Weak transcription	Stomach Mucosa	stomach
15	chr13:49551800-49557200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
16	chr13:49551800-49569400	Weak transcription	Psoas Muscle	Psoas
17	chr13:49552000-49555400	Enhancers	Primary B cells from peripheral blood	blood
18	chr13:49552200-49555200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
19	chr13:49552200-49555400	Enhancers	Primary monocytes fromperipheralblood	blood
20	chr13:49552200-49570400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr13:49552400-49554600	Enhancers	Fetal Intestine Small	intestine
22	chr13:49552400-49555600	Enhancers	Primary T helper cells fromperipheralblood	blood
23	chr13:49552400-49556200	Enhancers	HepG2	liver
24	chr13:49552400-49558000	Enhancers	Colon Smooth Muscle	Colon
25	chr13:49552600-49554200	Enhancers	Primary B cells from cord blood	blood
26	chr13:49552600-49554400	Enhancers	Liver	Liver
27	chr13:49552600-49554400	Enhancers	Dnd41	blood
28	chr13:49552600-49554600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
29	chr13:49552600-49554800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
30	chr13:49552600-49555000	Enhancers	Fetal Intestine Large	intestine
31	chr13:49552600-49555000	Enhancers	NHEK	skin
32	chr13:49552600-49555600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr13:49552800-49554600	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
34	chr13:49553000-49554200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr13:49553000-49555000	Enhancers	Primary hematopoietic stem cells short term culture	blood
36	chr13:49553200-49554200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr13:49553200-49554400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr13:49553200-49554400	Enhancers	Small Intestine	intestine
39	chr13:49553200-49554600	Enhancers	Aorta	Aorta
40	chr13:49553200-49554600	Active TSS	Left Ventricle	heart
41	chr13:49553200-49555000	Enhancers	Primary T cells from cord blood	blood
42	chr13:49553200-49555000	Enhancers	Primary hematopoietic stem cells	blood
43	chr13:49553400-49554200	Enhancers	Rectal Smooth Muscle	rectum
44	chr13:49553400-49554400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr13:49553400-49554600	Enhancers	H1 Cell Line	embryonic stem cell
46	chr13:49553400-49554600	Enhancers	Brain Anterior Caudate	brain
47	chr13:49553400-49564800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr13:49553600-49554200	Enhancers	Adipose Nuclei	Adipose
49	chr13:49553600-49554600	Active TSS	Duodenum Mucosa	Duodenum
50	chr13:49553600-49555000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--

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