Variant report

Variant	rs4943690
Chromosome Location	chr13:40237647-40237648
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	chr13:40228867..40231362-chr13:40235168..40238124,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000133103	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1006635	1.00[AMR][1000 genomes]
rs13378904	1.00[AMR][1000 genomes]
rs17060145	1.00[AMR][1000 genomes]
rs2324340	1.00[AMR][1000 genomes]
rs3000477	1.00[AMR][1000 genomes]
rs3000480	1.00[AMR][1000 genomes]
rs3000484	1.00[AMR][1000 genomes]
rs3000486	1.00[AMR][1000 genomes]
rs3012138	1.00[AMR][1000 genomes]
rs3012148	1.00[AMR][1000 genomes]
rs3012150	1.00[AMR][1000 genomes]
rs4268631	1.00[AMR][1000 genomes]
rs4318086	1.00[AMR][1000 genomes]
rs4324019	1.00[AMR][1000 genomes]
rs4326926	1.00[AMR][1000 genomes]
rs4383025	1.00[AMR][1000 genomes]
rs4488331	1.00[AMR][1000 genomes]
rs6563741	1.00[AMR][1000 genomes]
rs6563744	1.00[AMR][1000 genomes]
rs7319899	1.00[AMR][1000 genomes]
rs7333700	1.00[AMR][1000 genomes]
rs7336514	1.00[AMR][1000 genomes]
rs7490747	1.00[AMR][1000 genomes]
rs7996170	1.00[AMR][1000 genomes]
rs9315727	1.00[AMR][1000 genomes]
rs9532415	1.00[AMR][1000 genomes]
rs9532418	1.00[AMR][1000 genomes]
rs9532421	1.00[AMR][1000 genomes]
rs9548864	1.00[AMR][1000 genomes]
rs9594354	1.00[AMR][1000 genomes]
rs9603614	1.00[AMR][1000 genomes]
rs9805352	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1054600	chr13:39801283-40545027	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
2	nsv1054797	chr13:40198744-40618428	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	10 gene(s)	inside rSNPs	diseases
3	nsv541755	chr13:40198744-40618428	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	10 gene(s)	inside rSNPs	diseases
4	nsv832586	chr13:40222880-40379063	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA	6 gene(s)	inside rSNPs	diseases
5	nsv870429	chr13:40235061-40265634	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS	TF binding region Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:40230600-40252200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr13:40230600-40254600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr13:40230600-40254600	Weak transcription	Lung	lung
4	chr13:40230600-40254800	Weak transcription	Aorta	Aorta
5	chr13:40230600-40263800	Weak transcription	Spleen	Spleen
6	chr13:40230800-40238800	Weak transcription	Fetal Kidney	kidney
7	chr13:40230800-40238800	Weak transcription	HSMM	muscle
8	chr13:40230800-40239400	Weak transcription	HSMMtube	muscle
9	chr13:40230800-40239600	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr13:40230800-40239800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr13:40230800-40240000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr13:40230800-40246600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr13:40230800-40254600	Weak transcription	Left Ventricle	heart
14	chr13:40230800-40254600	Weak transcription	Psoas Muscle	Psoas
15	chr13:40230800-40254800	Weak transcription	Fetal Thymus	thymus
16	chr13:40230800-40256400	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr13:40230800-40258400	Weak transcription	Colonic Mucosa	Colon
18	chr13:40230800-40262000	Weak transcription	Thymus	Thymus
19	chr13:40230800-40275000	Weak transcription	Right Ventricle	heart
20	chr13:40231000-40237800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr13:40231000-40238800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
22	chr13:40231000-40239200	Weak transcription	Primary neutrophils fromperipheralblood	blood
23	chr13:40231000-40241600	Weak transcription	Hela-S3	cervix
24	chr13:40231000-40243800	Weak transcription	Fetal Heart	heart
25	chr13:40231000-40252200	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr13:40231000-40252800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr13:40231000-40254400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr13:40231000-40254400	Weak transcription	Stomach Smooth Muscle	stomach
29	chr13:40231000-40254600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
30	chr13:40231000-40254600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr13:40231000-40254600	Weak transcription	NHLF	lung
32	chr13:40231000-40256400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr13:40231000-40256400	Weak transcription	NHEK	skin
34	chr13:40231000-40257200	Weak transcription	HMEC	breast
35	chr13:40231000-40261800	Weak transcription	Brain Substantia Nigra	brain
36	chr13:40231000-40266200	Weak transcription	Rectal Smooth Muscle	rectum
37	chr13:40231000-40270800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr13:40231000-40286000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr13:40231200-40239600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr13:40231200-40254400	Weak transcription	Muscle Satellite Cultured Cells	--
41	chr13:40231200-40254600	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr13:40231200-40254800	Weak transcription	Fetal Stomach	stomach
43	chr13:40231400-40237800	Weak transcription	Fetal Muscle Leg	muscle
44	chr13:40231400-40253600	Weak transcription	Cortex derived primary cultured neurospheres	brain
45	chr13:40231400-40254600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr13:40231400-40264200	Weak transcription	Esophagus	oesophagus
47	chr13:40231400-40268000	Weak transcription	Small Intestine	intestine
48	chr13:40231600-40239800	Weak transcription	GM12878-XiMat	blood
49	chr13:40231600-40254400	Weak transcription	Fetal Brain Male	brain
50	chr13:40231600-40270200	Weak transcription	Gastric	stomach

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