Variant report

Variant	rs17692648
Chromosome Location	chr2:148687731-148687732
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:148686945..148688969-chr2:148693419..148695079,2	MCF-7	breast:
2	chr2:148679481..148681984-chr2:148684810..148687787,3	K562	blood:
3	chr2:148686777..148688417-chr2:148690685..148692251,2	MCF-7	breast:
4	chr2:148679983..148681513-chr2:148684810..148687747,2	K562	blood:

Extended variants
information (count: 57 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs1234398	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1234414	1.00[CEU][hapmap];0.92[CHB][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1234417	1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1234420	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1234423	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1424941	1.00[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1469211	0.82[ASW][hapmap];0.82[CEU][hapmap];0.93[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.93[LWK][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17218938	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17225402	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17225423	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17225430	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17232078	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17691284	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17693310	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17741344	0.86[ASN][1000 genomes]
rs17741978	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17742134	0.87[CEU][hapmap];0.92[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17742246	0.87[CEU][hapmap];0.92[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17742342	0.87[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17743157	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1994189	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3754541	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3820715	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60809905	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62169472	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62169473	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62169474	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62169477	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62169478	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62169479	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62169480	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62169481	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62169482	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62169483	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62169530	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62169531	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62169532	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62169550	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6430280	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6747792	1.00[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.92[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs721344	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs730356	0.89[ASN][1000 genomes]
rs7560502	1.00[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7574172	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs7595052	0.90[ASN][1000 genomes]
rs7602296	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs929940	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs981814	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv875275	chr2:148166428-148711242	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv916286	chr2:148438001-148977722	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv529388	chr2:148471340-148934846	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	esv3392562	chr2:148476961-148843061	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
5	nsv1009602	chr2:148668195-148844240	ZNF genes & repeats Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
6	nsv535967	chr2:148668195-148844240	Weak transcription Flanking Active TSS Strong transcription Genic enhancers Enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
7	nsv1000246	chr2:148669162-148780280	Weak transcription Strong transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
8	nsv535968	chr2:148669162-148780280	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
9	nsv535969	chr2:148677122-148715921	Strong transcription Weak transcription Genic enhancers Enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17692648	LYPD6	cis	cerebellum	SCAN

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:148637200-148752600	Weak transcription	Small Intestine	intestine
2	chr2:148646600-148691000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
3	chr2:148647200-148719600	Weak transcription	Pancreas	Pancrea
4	chr2:148650200-148719600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr2:148651200-148691600	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr2:148652800-148690000	Weak transcription	Primary hematopoietic stem cells	blood
7	chr2:148652800-148693600	Weak transcription	Lung	lung
8	chr2:148653200-148692000	Weak transcription	Ovary	ovary
9	chr2:148653200-148719600	Weak transcription	Esophagus	oesophagus
10	chr2:148654000-148690000	Weak transcription	Primary T cells from cord blood	blood
11	chr2:148658800-148741600	Weak transcription	Aorta	Aorta
12	chr2:148659600-148719800	Weak transcription	Gastric	stomach
13	chr2:148661600-148718200	Weak transcription	Fetal Intestine Small	intestine
14	chr2:148663000-148692200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr2:148664600-148721200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr2:148664800-148693800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr2:148668600-148691800	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr2:148670600-148690200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
19	chr2:148671200-148690200	Weak transcription	Placenta	Placenta
20	chr2:148671600-148690200	Weak transcription	Primary T cells fromperipheralblood	blood
21	chr2:148671800-148690200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr2:148671800-148691800	Weak transcription	NHLF	lung
23	chr2:148671800-148692000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr2:148671800-148698800	Weak transcription	NHEK	skin
25	chr2:148671800-148719600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr2:148672000-148691400	Weak transcription	Brain Anterior Caudate	brain
27	chr2:148672000-148692000	Weak transcription	Brain Substantia Nigra	brain
28	chr2:148672000-148692800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr2:148672000-148693000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr2:148672200-148688400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr2:148672200-148693800	Weak transcription	HUVEC	blood vessel
32	chr2:148672200-148695800	Weak transcription	Brain Cingulate Gyrus	brain
33	chr2:148672200-148706800	Weak transcription	Brain Germinal Matrix	brain
34	chr2:148672400-148688400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr2:148672400-148690000	Weak transcription	A549	lung
36	chr2:148672400-148692800	Weak transcription	Stomach Mucosa	stomach
37	chr2:148672800-148688400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr2:148672800-148688600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr2:148674400-148692000	Weak transcription	H1 Cell Line	embryonic stem cell
40	chr2:148675000-148690200	Weak transcription	Primary T helper cells fromperipheralblood	blood
41	chr2:148675400-148708800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr2:148676200-148722400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
43	chr2:148676600-148690400	Weak transcription	Primary B cells from cord blood	blood
44	chr2:148676600-148693600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
45	chr2:148677200-148696200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
46	chr2:148678000-148718200	Weak transcription	Right Ventricle	heart
47	chr2:148679000-148718800	Weak transcription	Fetal Stomach	stomach
48	chr2:148679600-148737200	Weak transcription	Hela-S3	cervix
49	chr2:148681000-148729600	Weak transcription	NHDF-Ad	bronchial
50	chr2:148681600-148688000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood

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