Variant report

Variant	rs6415604
Chromosome Location	chr8:66736695-66736696
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	chr8:66736038..66738314-chr8:66742925..66745716,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ARMC1-5	chr8:66736265-66738758	NONHSAT127001

Extended variants
information (count: 19 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs11782766	0.90[JPT][hapmap]
rs16932346	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1877640	0.90[JPT][hapmap]
rs2063685	0.90[JPT][hapmap]
rs6472222	0.90[JPT][hapmap]
rs6472225	0.90[JPT][hapmap]
rs6472226	0.82[JPT][hapmap]
rs6472227	1.00[CHB][hapmap];0.83[CHD][hapmap];0.90[JPT][hapmap];0.94[ASN][1000 genomes]
rs7005571	1.00[CHB][hapmap]
rs7014676	0.90[JPT][hapmap]
rs73242909	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73242913	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73242953	0.90[AMR][1000 genomes]
rs7821744	1.00[CHB][hapmap]
rs7828699	0.90[JPT][hapmap]
rs7829484	0.88[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.90[JPT][hapmap];0.88[MEX][hapmap];0.89[MKK][hapmap];0.86[TSI][hapmap];0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs972362	0.90[JPT][hapmap]
rs974149	0.90[JPT][hapmap]

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	esv1793412	chr8:66705321-66761366	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6415604	MTFR1	cis	parietal	SCAN
rs6415604	GGH	cis	parietal	SCAN
rs6415604	MTFR1	cis	cerebellum	SCAN

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:66713400-66738200	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr8:66716200-66738400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr8:66719400-66738600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr8:66719400-66750000	Weak transcription	Hela-S3	cervix
5	chr8:66720000-66736800	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr8:66720400-66744800	Weak transcription	NHEK	skin
7	chr8:66721400-66738000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr8:66723800-66738200	Weak transcription	Pancreas	Pancrea
9	chr8:66725200-66742000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr8:66725200-66747000	Weak transcription	NHDF-Ad	bronchial
11	chr8:66725400-66742000	Weak transcription	HMEC	breast
12	chr8:66725400-66751200	Weak transcription	Fetal Heart	heart
13	chr8:66727600-66737000	Weak transcription	Brain Angular Gyrus	brain
14	chr8:66729000-66744800	Weak transcription	Gastric	stomach
15	chr8:66729400-66738200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr8:66729400-66744800	Weak transcription	Spleen	Spleen
17	chr8:66729400-66749400	Weak transcription	Fetal Brain Male	brain
18	chr8:66730000-66741400	Weak transcription	Duodenum Mucosa	Duodenum
19	chr8:66730000-66741600	Weak transcription	Primary neutrophils fromperipheralblood	blood
20	chr8:66730800-66737400	Weak transcription	HUES64 Cell Line	embryonic stem cell
21	chr8:66731000-66752600	Weak transcription	Stomach Smooth Muscle	stomach
22	chr8:66731400-66741000	Weak transcription	Fetal Muscle Trunk	muscle
23	chr8:66731600-66738000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr8:66731600-66738200	Weak transcription	Lung	lung
25	chr8:66731600-66740000	Weak transcription	A549	lung
26	chr8:66731600-66741400	Weak transcription	Fetal Stomach	stomach
27	chr8:66731600-66752600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr8:66731800-66752600	Weak transcription	Adipose Nuclei	Adipose
29	chr8:66732200-66738000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr8:66732200-66738000	Weak transcription	HUES6 Cell Line	embryonic stem cell
31	chr8:66732200-66741400	Weak transcription	Fetal Intestine Large	intestine
32	chr8:66732400-66739200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr8:66732400-66745000	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr8:66732400-66745000	Weak transcription	Rectal Mucosa Donor 29	rectum
35	chr8:66732600-66738000	Weak transcription	Thymus	Thymus
36	chr8:66732600-66738800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr8:66732600-66739000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr8:66732600-66751000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr8:66732600-66751000	Weak transcription	Fetal Lung	lung
40	chr8:66732800-66736800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr8:66732800-66738200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
42	chr8:66733000-66738600	Weak transcription	Primary hematopoietic stem cells	blood
43	chr8:66733000-66752000	Weak transcription	Fetal Intestine Small	intestine
44	chr8:66733400-66743800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr8:66734200-66738600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
46	chr8:66734200-66742800	Enhancers	Primary T killer memory cells from peripheral blood	blood
47	chr8:66734400-66740200	Genic enhancers	Primary T helper memory cells from peripheral blood 1	blood
48	chr8:66734800-66736800	Weak transcription	Skeletal Muscle Female	skeletal muscle
49	chr8:66734800-66737000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
50	chr8:66734800-66738000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood

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