Variant report

Variant	rs17791808
Chromosome Location	chr6:114242419-114242420
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	chr6:114241819..114244769-chr6:114245908..114248652,2	K562	blood:
2	chr6:114200223..114202562-chr6:114240736..114243361,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MARCKS-1	chr6:114241620-114242806	XLOC_005438
2	lnc-MARCKS-1	chr6:114241620-114242806	ENSG00000175967.3

Extended variants
information (count: 15 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs11391	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1322454	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17794523	1.00[YRI][hapmap]
rs1889555	1.00[ASW][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap]
rs3778215	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56168685	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs58052068	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72948645	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73766806	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73766809	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73766810	0.86[EUR][1000 genomes];0.92[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	nsv1021774	chr6:114063971-114407280	Enhancers Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
2	nsv538422	chr6:114063971-114407280	Genic enhancers Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
3	esv3363275	chr6:114101331-114302866	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
4	nsv830779	chr6:114206534-114246099	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17791808	HDAC2	cis	cerebellum	SCAN
rs17791808	PTPN5	trans	parietal	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:114226600-114246000	Weak transcription	Fetal Stomach	stomach
2	chr6:114240600-114243000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
3	chr6:114241600-114242600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr6:114241600-114242800	Enhancers	Primary hematopoietic stem cells short term culture	blood
5	chr6:114241600-114242800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr6:114241800-114242600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr6:114241800-114242600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
8	chr6:114241800-114242800	Flanking Active TSS	K562	blood
9	chr6:114241800-114243000	Enhancers	HUVEC	blood vessel
10	chr6:114242000-114242600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr6:114242000-114242600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
12	chr6:114242000-114242600	Enhancers	Primary T killer memory cells from peripheral blood	blood
13	chr6:114242000-114242800	Enhancers	Fetal Intestine Small	intestine
14	chr6:114242000-114242800	Enhancers	Left Ventricle	heart
15	chr6:114242000-114242800	Enhancers	Right Atrium	heart
16	chr6:114242000-114243000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr6:114242000-114243000	Enhancers	Fetal Muscle Leg	muscle
18	chr6:114242400-114242800	Enhancers	HepG2	liver
19	chr6:114242400-114244800	Weak transcription	Fetal Lung	lung
20	chr6:114242400-114245600	Weak transcription	Adipose Nuclei	Adipose
21	chr6:114242400-114245800	Weak transcription	Primary hematopoietic stem cells	blood
22	chr6:114242400-114265400	Weak transcription	Thymus	Thymus

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