Variant report

Variant	rs11719995
Chromosome Location	chr3:51593827-51593828
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:51593552..51596365-chr3:51596602..51598437,2	K562	blood:

Extended variants
information (count: 29 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1055429	0.84[EUR][1000 genomes]
rs11709482	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11917683	1.00[CEU][hapmap]
rs11919197	0.85[CEU][hapmap]
rs13090011	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.96[MEX][hapmap];0.97[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap]
rs1542574	0.88[ASW][hapmap];1.00[CEU][hapmap];0.80[GIH][hapmap];0.87[LWK][hapmap];0.86[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap]
rs1552074	0.92[CEU][hapmap]
rs2127655	0.92[CEU][hapmap]
rs2164599	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3821829	0.85[CEU][hapmap]
rs4067	0.85[CEU][hapmap]
rs4234644	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.89[EUR][1000 genomes]
rs4355273	0.85[CEU][hapmap]
rs4494918	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4687721	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs4687770	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.83[MKK][hapmap]
rs4687771	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6775666	0.85[CEU][hapmap]
rs6787312	1.00[CEU][hapmap]
rs6809155	0.82[EUR][1000 genomes]
rs7625821	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9841077	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9864443	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9864693	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9866430	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[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	nsv1014464	chr3:51220151-51909780	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer 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	53 gene(s)	inside rSNPs	diseases
2	nsv997264	chr3:51584056-51689648	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv536570	chr3:51584056-51689648	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv999553	chr3:51584056-51696052	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs11719995	HYAL2	cis	parietal	SCAN
rs11719995	TEX264	cis	Nerve Tibial	GTEx
rs11719995	TEX264	cis	Esophagus Muscularis	GTEx
rs11719995	HEMK1	cis	cerebellum	SCAN
rs11719995	IQCF2	cis	parietal	SCAN
rs11719995	MST1	cis	cerebellum	SCAN
rs11719995	TEX264	cis	Artery Tibial	GTEx

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:51573800-51594000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr3:51574000-51597000	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr3:51574000-51600600	Weak transcription	Gastric	stomach
4	chr3:51574000-51615400	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr3:51574000-51624800	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr3:51574200-51616400	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr3:51574400-51613800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr3:51574600-51594400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr3:51574600-51600800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr3:51574600-51601800	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr3:51574600-51624600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr3:51574800-51597600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr3:51574800-51624800	Weak transcription	NH-A	brain
14	chr3:51575000-51597400	Weak transcription	Small Intestine	intestine
15	chr3:51575200-51615600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr3:51576000-51595400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
17	chr3:51576400-51597800	Weak transcription	HUES48 Cell Line	embryonic stem cell
18	chr3:51576400-51602000	Weak transcription	Brain Hippocampus Middle	brain
19	chr3:51577200-51597600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr3:51578600-51607000	Weak transcription	HUES64 Cell Line	embryonic stem cell
21	chr3:51578800-51597400	Weak transcription	Primary hematopoietic stem cells	blood
22	chr3:51578800-51600200	Weak transcription	A549	lung
23	chr3:51578800-51624400	Weak transcription	Esophagus	oesophagus
24	chr3:51579000-51602000	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr3:51579200-51602400	Weak transcription	HMEC	breast
26	chr3:51580000-51602600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr3:51584200-51600200	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr3:51584200-51602200	Weak transcription	Pancreas	Pancrea
29	chr3:51584200-51602200	Weak transcription	Spleen	Spleen
30	chr3:51584200-51614200	Weak transcription	Aorta	Aorta
31	chr3:51584600-51597000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
32	chr3:51584800-51600200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr3:51584800-51602200	Weak transcription	Brain Cingulate Gyrus	brain
34	chr3:51585000-51615600	Weak transcription	NHEK	skin
35	chr3:51585200-51624400	Weak transcription	Brain Germinal Matrix	brain
36	chr3:51585400-51594200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr3:51585400-51602000	Weak transcription	Primary neutrophils fromperipheralblood	blood
38	chr3:51585800-51612400	Weak transcription	Fetal Thymus	thymus
39	chr3:51585800-51625000	Weak transcription	Colonic Mucosa	Colon
40	chr3:51586200-51600000	Weak transcription	Stomach Mucosa	stomach
41	chr3:51586400-51601800	Weak transcription	Cortex derived primary cultured neurospheres	brain
42	chr3:51586800-51594000	Strong transcription	Primary B cells from cord blood	blood
43	chr3:51586800-51595800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr3:51586800-51595800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr3:51587000-51594200	Strong transcription	Monocytes-CD14+_RO01746	blood
46	chr3:51587400-51595600	Strong transcription	Primary T cells from cord blood	blood
47	chr3:51587800-51607000	Weak transcription	Primary T cells fromperipheralblood	blood
48	chr3:51587800-51624400	Weak transcription	Hela-S3	cervix
49	chr3:51588000-51612600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr3:51588000-51640000	Weak transcription	Primary T killer memory cells from peripheral blood	blood

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