Variant report

Variant	rs793654
Chromosome Location	chr6:24404334-24404335
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	chr6:24402909..24405943-chr6:24492830..24496087,3	K562	blood:
2	chr6:24401784..24404907-chr6:24494976..24497958,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000112294	Chromatin interaction
ENSG00000112293	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs1056283	0.93[CHD][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs1277343	0.84[ASN][1000 genomes]
rs1277346	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1321819	0.81[ASN][1000 genomes]
rs13218564	0.81[GIH][hapmap]
rs13735	0.93[CHD][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs1742280	0.82[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs1772253	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs2753922	0.97[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs2793422	1.00[ASW][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs2876672	0.86[ASN][1000 genomes]
rs3827640	0.93[CHD][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs6920147	0.88[JPT][hapmap];0.84[ASN][1000 genomes]
rs6936856	0.83[ASN][1000 genomes]
rs7746747	0.85[YRI][hapmap]
rs7769012	0.84[ASN][1000 genomes]
rs793652	0.97[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs793657	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs793679	0.85[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs793680	0.90[CHD][hapmap]
rs793682	0.82[ASN][1000 genomes]
rs793688	0.87[CHD][hapmap]
rs793690	0.82[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs9393554	0.93[CHD][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1026638	chr6:24347972-24475300	Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs793654	MRS2L	cis	multi-tissue	Pritchard
rs793654	MRS2	cis	lymphoblastoid	seeQTL
rs793654	ALDH5A1	cis	cerebellum	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:24401800-24405400	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr6:24402400-24406600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
3	chr6:24402600-24404400	Active TSS	Brain Cingulate Gyrus	brain
4	chr6:24402600-24404400	Active TSS	A549	lung
5	chr6:24402600-24404600	Flanking Active TSS	Adipose Nuclei	Adipose
6	chr6:24402600-24404600	Active TSS	Rectal Smooth Muscle	rectum
7	chr6:24402600-24404600	Active TSS	Stomach Smooth Muscle	stomach
8	chr6:24402600-24404800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr6:24402600-24405000	Active TSS	H1 Cell Line	embryonic stem cell
10	chr6:24402600-24405200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr6:24402600-24405400	Active TSS	H9 Cell Line	embryonic stem cell
12	chr6:24402600-24405600	Active TSS	GM12878-XiMat	blood
13	chr6:24402800-24404400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr6:24402800-24404400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr6:24402800-24404400	Active TSS	Brain Inferior Temporal Lobe	brain
16	chr6:24402800-24404400	Active TSS	Fetal Intestine Small	intestine
17	chr6:24402800-24404400	Active TSS	Left Ventricle	heart
18	chr6:24402800-24404600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr6:24402800-24404600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr6:24402800-24404600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
21	chr6:24402800-24404600	Flanking Active TSS	Primary hematopoietic stem cells	blood
22	chr6:24402800-24404600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr6:24402800-24404600	Active TSS	Colon Smooth Muscle	Colon
24	chr6:24402800-24404600	Active TSS	Psoas Muscle	Psoas
25	chr6:24402800-24404600	Active TSS	Right Atrium	heart
26	chr6:24402800-24404600	Active TSS	Right Ventricle	heart
27	chr6:24402800-24404600	Active TSS	HSMMtube	muscle
28	chr6:24402800-24404600	Active TSS	NHLF	lung
29	chr6:24402800-24405400	Active TSS	iPS-15b Cell Line	embryonic stem cell
30	chr6:24402800-24405400	Active TSS	iPS-20b Cell Line	embryonic stem cell
31	chr6:24402800-24405800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr6:24403000-24404400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr6:24403000-24404400	Active TSS	Ovary	ovary
34	chr6:24403000-24404600	Active TSS	Fetal Intestine Large	intestine
35	chr6:24403000-24404600	Active TSS	Fetal Stomach	stomach
36	chr6:24403000-24404800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr6:24403000-24404800	Active TSS	HMEC	breast
38	chr6:24403000-24405000	Active TSS	HUES48 Cell Line	embryonic stem cell
39	chr6:24403000-24405400	Active TSS	HUES64 Cell Line	embryonic stem cell
40	chr6:24403200-24404400	Active TSS	Colonic Mucosa	Colon
41	chr6:24403200-24404400	Active TSS	Fetal Thymus	thymus
42	chr6:24403200-24404400	Active TSS	NHDF-Ad	bronchial
43	chr6:24403400-24404400	Active TSS	Skeletal Muscle Female	skeletal muscle
44	chr6:24403400-24404600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr6:24403400-24404800	Flanking Active TSS	Primary B cells from cord blood	blood
46	chr6:24403600-24404400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr6:24403600-24404400	Flanking Active TSS	Brain Germinal Matrix	brain
48	chr6:24403800-24404400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
49	chr6:24403800-24404400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr6:24403800-24404400	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland

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