Variant report

Variant	rs3506
Chromosome Location	chr17:33987034-33987035
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	chr17:33984816..33987064-chr17:33989819..33992082,2	K562	blood:

Extended variants
information (count: 58 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs11650225	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11650621	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11651380	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11652390	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11653354	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11654542	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11655098	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap]
rs11656872	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11657558	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12451876	1.00[CHB][hapmap]
rs12936539	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12936693	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12939138	1.00[ASW][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12939481	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12940422	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12940584	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12941376	1.00[YRI][hapmap]
rs12943224	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12945102	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12945419	1.00[YRI][hapmap]
rs12945980	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12947274	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12949877	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12950534	0.91[AFR][1000 genomes]
rs12951703	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1350010	1.00[CHB][hapmap]
rs17606150	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17608253	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17638076	0.82[AFR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17669281	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17670584	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17670614	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17676508	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs321600	0.86[MKK][hapmap]
rs34063751	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34296197	0.82[AFR][1000 genomes]
rs34528380	0.91[AFR][1000 genomes]
rs34874930	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34937989	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35396673	0.82[AFR][1000 genomes]
rs35419374	0.91[AFR][1000 genomes]
rs35515868	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35672532	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35774966	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35872249	0.91[AFR][1000 genomes]
rs4531775	0.82[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs71381460	1.00[ASN][1000 genomes]
rs71381461	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71381463	0.97[EUR][1000 genomes]
rs71381464	0.82[AFR][1000 genomes]
rs71381465	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71381467	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71381469	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8066132	1.00[CHB][hapmap]

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	nsv534371	chr17:33456878-34094068	Strong transcription Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	137 gene(s)	inside rSNPs	diseases
2	nsv908079	chr17:33849869-34034851	Active TSS Strong transcription Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
3	nsv1060890	chr17:33884124-34011034	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
4	nsv543318	chr17:33884124-34011034	Genic enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3506	SRPK1	trans	parietal	SCAN
rs3506	TMEM132E	cis	parietal	SCAN
rs3506	SPACA3	cis	cerebellum	SCAN
rs3506	PEX12	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:33916800-34001200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr17:33921000-34024400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr17:33931000-34040200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr17:33933000-33997800	Weak transcription	Esophagus	oesophagus
5	chr17:33948800-34010600	Strong transcription	Primary monocytes fromperipheralblood	blood
6	chr17:33949200-34001200	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr17:33954600-34001800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr17:33954600-34006000	Weak transcription	Stomach Mucosa	stomach
9	chr17:33958200-33992400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr17:33958200-33992400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr17:33960000-34024600	Strong transcription	Primary T helper cells fromperipheralblood	blood
12	chr17:33960200-33987600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr17:33963400-34001200	Weak transcription	Aorta	Aorta
14	chr17:33966000-34002000	Strong transcription	Primary T cells from cord blood	blood
15	chr17:33968000-33997600	Weak transcription	HSMMtube	muscle
16	chr17:33968000-34055800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr17:33968400-33997800	Weak transcription	Brain Substantia Nigra	brain
18	chr17:33969000-33989800	Weak transcription	Psoas Muscle	Psoas
19	chr17:33969000-34001200	Weak transcription	Right Ventricle	heart
20	chr17:33969400-34001200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr17:33969600-33997600	Weak transcription	Brain Anterior Caudate	brain
22	chr17:33969600-33998600	Weak transcription	Fetal Brain Male	brain
23	chr17:33970000-33995400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
24	chr17:33970000-33997800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr17:33970400-33987600	Weak transcription	Fetal Heart	heart
26	chr17:33970400-34001200	Weak transcription	Small Intestine	intestine
27	chr17:33971200-33992000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr17:33971200-33997800	Weak transcription	Colon Smooth Muscle	Colon
29	chr17:33972000-33990600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr17:33972000-33998800	Weak transcription	Ovary	ovary
31	chr17:33974400-33992600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
32	chr17:33975000-34025800	Strong transcription	Primary B cells from peripheral blood	blood
33	chr17:33975400-33992800	Strong transcription	Primary B cells from cord blood	blood
34	chr17:33975600-33991400	Strong transcription	Primary T helper cells PMA-I stimulated	--
35	chr17:33976600-33991600	Strong transcription	Rectal Mucosa Donor 29	rectum
36	chr17:33976800-33988800	Strong transcription	HUES6 Cell Line	embryonic stem cell
37	chr17:33977000-33994600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
38	chr17:33977200-33988200	Strong transcription	Dnd41	blood
39	chr17:33977200-33993800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
40	chr17:33977200-34010400	Strong transcription	Monocytes-CD14+_RO01746	blood
41	chr17:33977400-33988000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr17:33977400-33988400	Strong transcription	Primary T cells fromperipheralblood	blood
43	chr17:33977800-33990600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr17:33977800-33990600	Weak transcription	Spleen	Spleen
45	chr17:33977800-33997800	Weak transcription	Gastric	stomach
46	chr17:33978000-33990400	Weak transcription	Skeletal Muscle Female	skeletal muscle
47	chr17:33978000-33990600	Weak transcription	H9 Cell Line	embryonic stem cell
48	chr17:33978000-33997800	Weak transcription	Lung	lung
49	chr17:33978000-34001200	Weak transcription	Brain Angular Gyrus	brain
50	chr17:33978200-33989600	Weak transcription	Thymus	Thymus

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