Variant report

Variant	rs11619804
Chromosome Location	chr13:49888131-49888132
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:49885803..49888221-chr13:49971631..49973979,2	MCF-7	breast:
2	chr13:49882439..49884408-chr13:49887006..49888853,2	MCF-7	breast:
3	chr13:49886161..49888656-chr13:49974346..49978416,3	MCF-7	breast:
4	chr13:49879463..49882852-chr13:49885235..49888235,4	MCF-7	breast:
5	chr13:49886834..49889531-chr13:50158388..50161122,2	K562	blood:

Variant related genes	Relation type
ENSG00000136144	Chromatin interaction
ENSG00000102547	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs11838927	0.93[ASN][1000 genomes]
rs11843587	0.92[ASN][1000 genomes]
rs12585196	0.83[CHB][hapmap]
rs1555672	0.90[CHB][hapmap];0.88[CHD][hapmap];0.91[JPT][hapmap];0.91[ASN][1000 genomes]
rs2147398	0.83[CHB][hapmap]
rs2181905	0.89[ASN][1000 genomes]
rs2407521	0.82[CHB][hapmap];0.81[CHD][hapmap];0.87[JPT][hapmap];0.81[ASN][1000 genomes]
rs4941637	0.95[CHB][hapmap];0.91[JPT][hapmap];0.91[ASN][1000 genomes]
rs4942815	0.95[CHB][hapmap];0.91[JPT][hapmap];0.94[ASN][1000 genomes]
rs6561511	0.80[CHB][hapmap]
rs7330892	0.90[CHB][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs9535179	0.82[JPT][hapmap]
rs9535197	0.95[CHB][hapmap];0.82[JPT][hapmap];0.91[ASN][1000 genomes]
rs9535198	0.90[CHB][hapmap];0.91[JPT][hapmap];0.93[ASN][1000 genomes]
rs9535199	0.90[CHB][hapmap];0.91[JPT][hapmap];0.93[ASN][1000 genomes]
rs9535200	0.93[ASN][1000 genomes]
rs9591249	0.82[CHB][hapmap];0.81[CHD][hapmap];0.87[JPT][hapmap];0.81[ASN][1000 genomes]
rs9596077	0.84[ASN][1000 genomes]
rs9596079	0.93[ASN][1000 genomes]
rs9596082	0.90[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	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	nsv832607	chr13:49756458-49920894	Flanking Bivalent TSS/Enh Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
3	nsv900069	chr13:49815405-49976393	Strong transcription Enhancers Weak transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11619804	INTS6	cis	cerebellum	SCAN
rs11619804	CDADC1	cis	parietal	SCAN
rs11619804	CAB39L	cis	cerebellum	SCAN
rs11619804	SNORA31	cis	cerebellum	SCAN

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:49875800-49891000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr13:49876200-49895000	Weak transcription	Primary T cells fromperipheralblood	blood
3	chr13:49876200-49935600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr13:49878200-49893600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr13:49878200-49894800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr13:49880400-49894200	Weak transcription	Primary B cells from cord blood	blood
7	chr13:49880600-49888600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr13:49880600-49896000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr13:49881800-49906800	Weak transcription	Fetal Brain Male	brain
10	chr13:49884400-49888200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr13:49884600-49895000	Weak transcription	Primary hematopoietic stem cells	blood
12	chr13:49884600-49933600	Weak transcription	Brain Cingulate Gyrus	brain
13	chr13:49884800-49903800	Weak transcription	Fetal Brain Female	brain
14	chr13:49884800-49914200	Weak transcription	Brain Hippocampus Middle	brain
15	chr13:49884800-49925600	Weak transcription	Brain Substantia Nigra	brain
16	chr13:49885000-49895000	Weak transcription	Primary T helper cells fromperipheralblood	blood
17	chr13:49885400-49888400	Weak transcription	Fetal Stomach	stomach
18	chr13:49885600-49933400	Weak transcription	Primary T cells from cord blood	blood
19	chr13:49885800-49926000	Weak transcription	Brain Germinal Matrix	brain
20	chr13:49887400-49889800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr13:49887600-49888400	Enhancers	Muscle Satellite Cultured Cells	--
22	chr13:49887600-49888400	Enhancers	NH-A	brain
23	chr13:49887600-49888400	Enhancers	NHDF-Ad	bronchial
24	chr13:49887600-49889000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr13:49887600-49889000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
26	chr13:49887600-49889200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr13:49887600-49889200	Enhancers	HUVEC	blood vessel
28	chr13:49887600-49889400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr13:49887600-49889400	Enhancers	HMEC	breast
30	chr13:49887600-49889400	Enhancers	HSMM	muscle
31	chr13:49887600-49889400	Enhancers	HSMMtube	muscle
32	chr13:49887600-49889600	Enhancers	NHLF	lung
33	chr13:49887600-49889600	Enhancers	Osteobl	bone
34	chr13:49887800-49888200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr13:49887800-49888200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr13:49887800-49888200	Enhancers	Small Intestine	intestine
37	chr13:49887800-49888400	Enhancers	Primary hematopoietic stem cells short term culture	blood
38	chr13:49887800-49888400	Enhancers	Adipose Nuclei	Adipose
39	chr13:49887800-49888400	Enhancers	Brain Angular Gyrus	brain
40	chr13:49887800-49888400	Enhancers	Fetal Muscle Trunk	muscle
41	chr13:49887800-49888400	Enhancers	Fetal Muscle Leg	muscle
42	chr13:49887800-49888400	Enhancers	Gastric	stomach
43	chr13:49887800-49888400	Enhancers	Psoas Muscle	Psoas
44	chr13:49887800-49888400	Enhancers	Right Ventricle	heart
45	chr13:49887800-49888400	Flanking Active TSS	Hela-S3	cervix
46	chr13:49887800-49888600	Enhancers	ES-I3 Cell Line	embryonic stem cell
47	chr13:49887800-49888600	Enhancers	HUES6 Cell Line	embryonic stem cell
48	chr13:49887800-49888600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr13:49887800-49888600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr13:49887800-49888600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin

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