Variant report

Variant	rs17051685
Chromosome Location	chr3:51316220-51316221
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs12487468	1.00[YRI][hapmap]
rs12492615	1.00[ASW][hapmap];1.00[YRI][hapmap]
rs12493323	0.81[AFR][1000 genomes]
rs12495561	0.90[YRI][hapmap]
rs1480366	1.00[ASW][hapmap];0.91[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17051799	1.00[ASW][hapmap]
rs17051802	1.00[ASW][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs2170177	1.00[ASW][hapmap];0.91[YRI][hapmap]
rs4130473	1.00[YRI][hapmap]
rs4346580	1.00[ASW][hapmap];0.91[YRI][hapmap]
rs4974112	1.00[ASW][hapmap];0.91[YRI][hapmap];0.81[AFR][1000 genomes]
rs57019473	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58807639	1.00[AMR][1000 genomes]
rs59307262	1.00[AMR][1000 genomes]
rs61578076	1.00[AMR][1000 genomes]
rs72943888	1.00[AMR][1000 genomes]
rs72945711	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72945738	1.00[AMR][1000 genomes]
rs72945741	1.00[AMR][1000 genomes]
rs72951454	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72951466	1.00[AMR][1000 genomes]
rs72951469	1.00[AMR][1000 genomes]
rs72951474	1.00[AMR][1000 genomes]
rs72951478	1.00[AMR][1000 genomes]
rs880477	1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9880909	1.00[ASW][hapmap]

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	nsv1005858	chr3:51090373-51444027	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv536569	chr3:51090373-51444027	Flanking Active TSS Strong transcription Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	19 gene(s)	inside rSNPs	diseases
3	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17051685	HEMK1	cis	lymphoblastoid	seeQTL

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:51288200-51319200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr3:51296400-51318800	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr3:51297000-51317400	Weak transcription	HUES6 Cell Line	embryonic stem cell
4	chr3:51298000-51320800	Weak transcription	Stomach Smooth Muscle	stomach
5	chr3:51298400-51319000	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr3:51299600-51320800	Weak transcription	Brain Germinal Matrix	brain
7	chr3:51304400-51317400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr3:51305000-51318800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr3:51308200-51323000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr3:51311200-51319200	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr3:51311800-51316800	Weak transcription	Brain Anterior Caudate	brain
12	chr3:51312200-51319000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr3:51312200-51319200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr3:51313000-51322800	Weak transcription	HSMMtube	muscle
15	chr3:51313000-51323800	Weak transcription	Fetal Brain Male	brain
16	chr3:51313200-51316600	Weak transcription	Brain Substantia Nigra	brain
17	chr3:51313200-51317000	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr3:51313200-51317400	Weak transcription	Brain Angular Gyrus	brain
19	chr3:51313400-51321800	Weak transcription	Right Ventricle	heart
20	chr3:51313400-51322800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr3:51313800-51317400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr3:51314200-51317400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
23	chr3:51315400-51317200	Weak transcription	Brain Cingulate Gyrus	brain
24	chr3:51315400-51350000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr3:51315600-51319000	Weak transcription	Pancreatic Islets	Pancreatic Islet
26	chr3:51315800-51316800	Weak transcription	Brain Hippocampus Middle	brain
27	chr3:51316000-51317200	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr3:51316000-51320600	Weak transcription	Fetal Brain Female	brain

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