Variant report

Variant	rs17757406
Chromosome Location	chr19:18867561-18867562
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:18867338..18869538-chr19:18987734..18990558,2	K562	blood:
2	chr19:18859108..18863063-chr19:18866174..18869359,4	MCF-7	breast:
3	chr19:18866490..18868297-chr19:18882413..18884111,2	K562	blood:

Extended variants
information (count: 34 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs12609934	0.82[EUR][1000 genomes]
rs12975249	0.83[ASN][1000 genomes]
rs2075017	0.85[CEU][hapmap];0.86[GIH][hapmap];0.82[JPT][hapmap];0.92[MEX][hapmap];0.94[TSI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2240014	0.84[TSI][hapmap];0.82[EUR][1000 genomes]
rs2240887	0.89[ASW][hapmap];0.94[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.87[TSI][hapmap];0.88[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28494505	0.81[EUR][1000 genomes]
rs3746266	0.84[EUR][1000 genomes]
rs4808155	0.80[EUR][1000 genomes]
rs4808852	1.00[GIH][hapmap];0.92[MEX][hapmap];0.91[TSI][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4808853	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs56090467	0.80[EUR][1000 genomes]
rs56182405	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs56210931	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs57962499	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs58406187	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs61447117	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6510997	0.85[CEU][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.92[MEX][hapmap];0.94[TSI][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6510998	0.83[CEU][hapmap];0.88[GIH][hapmap];0.82[JPT][hapmap];0.92[MEX][hapmap];0.89[TSI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6510999	0.85[CEU][hapmap];0.89[GIH][hapmap];0.82[JPT][hapmap];0.92[MEX][hapmap];0.94[TSI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6511000	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6511001	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6511002	0.83[CHB][hapmap];0.87[ASN][1000 genomes]
rs7251560	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7251710	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7252217	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7256502	0.85[CEU][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.92[MEX][hapmap];0.94[TSI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7257846	0.84[GIH][hapmap];0.84[TSI][hapmap];0.82[EUR][1000 genomes]
rs7258259	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73537985	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs73537994	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs73537995	0.90[AMR][1000 genomes];0.92[EUR][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	nsv1057795	chr19:18453362-18883844	Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
2	nsv543925	chr19:18453362-18883844	Weak transcription Genic enhancers Strong transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
3	nsv911282	chr19:18624964-18928480	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs17757406	NDUFA13	cis	parietal	SCAN
rs17757406	DDA1	cis	cerebellum	SCAN
rs17757406	CRTC1	cis	cerebellum	SCAN

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:18844200-18872800	Weak transcription	Muscle Satellite Cultured Cells	--
2	chr19:18844600-18872800	Weak transcription	NH-A	brain
3	chr19:18844800-18871800	Weak transcription	Rectal Smooth Muscle	rectum
4	chr19:18846800-18871600	Weak transcription	Fetal Brain Male	brain
5	chr19:18846800-18872400	Weak transcription	Colon Smooth Muscle	Colon
6	chr19:18849200-18873000	Weak transcription	Psoas Muscle	Psoas
7	chr19:18854400-18873200	Weak transcription	NHLF	lung
8	chr19:18854600-18872800	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr19:18854600-18895800	Weak transcription	Right Atrium	heart
10	chr19:18854800-18872800	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr19:18856600-18872200	Weak transcription	Fetal Heart	heart
12	chr19:18857200-18873600	Weak transcription	Fetal Kidney	kidney
13	chr19:18858000-18867600	Weak transcription	Fetal Thymus	thymus
14	chr19:18859800-18868000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr19:18859800-18868000	Strong transcription	Fetal Brain Female	brain
16	chr19:18859800-18868200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr19:18860200-18868000	Strong transcription	Monocytes-CD14+_RO01746	blood
18	chr19:18860200-18868600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr19:18860400-18868200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr19:18861000-18868000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr19:18861000-18869400	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr19:18861200-18872600	Weak transcription	HUES64 Cell Line	embryonic stem cell
23	chr19:18861200-18873000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr19:18861600-18867600	Weak transcription	HUES6 Cell Line	embryonic stem cell
25	chr19:18861600-18868600	Strong transcription	Fetal Muscle Trunk	muscle
26	chr19:18861600-18873000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr19:18861600-18873000	Weak transcription	Brain Angular Gyrus	brain
28	chr19:18861600-18875200	Weak transcription	Primary T cells fromperipheralblood	blood
29	chr19:18861800-18868600	Strong transcription	Fetal Muscle Leg	muscle
30	chr19:18861800-18872800	Weak transcription	Brain Substantia Nigra	brain
31	chr19:18862000-18872600	Weak transcription	Liver	Liver
32	chr19:18862000-18872600	Weak transcription	Brain Anterior Caudate	brain
33	chr19:18862000-18872800	Weak transcription	Duodenum Mucosa	Duodenum
34	chr19:18862000-18875200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
35	chr19:18862600-18869200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
36	chr19:18862600-18872800	Weak transcription	Right Ventricle	heart
37	chr19:18862600-18888400	Weak transcription	Aorta	Aorta
38	chr19:18862800-18867800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr19:18862800-18873000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr19:18863200-18871800	Strong transcription	Fetal Stomach	stomach
41	chr19:18864600-18871800	Weak transcription	Cortex derived primary cultured neurospheres	brain
42	chr19:18864600-18872600	Weak transcription	Colonic Mucosa	Colon
43	chr19:18864600-18873200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr19:18864600-18873200	Weak transcription	Osteobl	bone
45	chr19:18864600-18887400	Weak transcription	Primary B cells from cord blood	blood
46	chr19:18864800-18869200	Weak transcription	Spleen	Spleen
47	chr19:18864800-18873000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
48	chr19:18864800-18875200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr19:18865000-18885000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
50	chr19:18865200-18867800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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