Variant report

Variant	rs6693408
Chromosome Location	chr1:184520728-184520729
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:184514258..184517893-chr1:184518659..184523395,6	MCF-7	breast:

Extended variants
information (count: 40 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10399817	0.94[CHB][hapmap];0.82[GIH][hapmap]
rs10489729	0.86[ASW][hapmap];0.83[CHD][hapmap];0.86[MKK][hapmap];0.86[ASN][1000 genomes]
rs10911610	0.94[CHB][hapmap];0.81[JPT][hapmap];0.91[ASN][1000 genomes]
rs11810399	0.80[CEU][hapmap]
rs12097916	0.83[ASN][1000 genomes]
rs12117823	0.87[CEU][hapmap];0.94[CHB][hapmap];0.93[TSI][hapmap];0.86[EUR][1000 genomes]
rs12120604	0.94[CHB][hapmap];0.88[GIH][hapmap];0.81[ASN][1000 genomes]
rs12121612	0.94[CHB][hapmap]
rs12127697	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.96[TSI][hapmap];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12129904	0.93[CEU][hapmap];0.94[CHB][hapmap];0.80[EUR][1000 genomes]
rs12138103	0.86[CEU][hapmap];1.00[CHB][hapmap];0.86[EUR][1000 genomes]
rs12141469	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12143271	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1535132	0.87[CEU][hapmap];0.94[CHB][hapmap];0.80[EUR][1000 genomes]
rs16823195	0.94[CHB][hapmap];0.88[GIH][hapmap]
rs16823197	0.87[CEU][hapmap];0.94[CHB][hapmap];1.00[GIH][hapmap];0.93[TSI][hapmap];0.86[EUR][1000 genomes]
rs16823238	0.94[CHB][hapmap];0.88[GIH][hapmap]
rs16823311	0.85[ASN][1000 genomes]
rs16823313	0.85[CHB][hapmap];0.83[CHD][hapmap];0.85[ASN][1000 genomes]
rs16823318	0.80[CHB][hapmap];0.81[CHD][hapmap]
rs1969683	0.85[ASN][1000 genomes]
rs2180072	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2207526	0.94[CHB][hapmap];0.82[GIH][hapmap]
rs2207527	0.87[CEU][hapmap];0.89[CHB][hapmap];1.00[GIH][hapmap];0.90[TSI][hapmap];0.87[EUR][1000 genomes]
rs35682339	0.98[ASN][1000 genomes]
rs57780220	0.83[ASN][1000 genomes]
rs61643431	0.86[ASN][1000 genomes]
rs61825202	0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61825204	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61825205	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61825239	0.81[ASN][1000 genomes]
rs6659261	0.94[CHB][hapmap];0.86[CHD][hapmap];0.87[GIH][hapmap];0.81[ASN][1000 genomes]
rs6669940	0.85[ASN][1000 genomes]
rs6683932	0.93[ASW][hapmap];0.94[CHB][hapmap];0.86[CHD][hapmap];0.88[GIH][hapmap];0.86[MKK][hapmap];0.80[ASN][1000 genomes]
rs7513091	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.96[TSI][hapmap];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7525267	0.80[ASN][1000 genomes]
rs7530615	0.85[ASN][1000 genomes]
rs7548188	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530079	chr1:183797938-184639971	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	esv2756618	chr1:184393343-184674343	Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Weak transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6693408	MR1	cis	cerebellum	SCAN
rs6693408	TDRD5	cis	parietal	SCAN

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:184502600-184527200	Weak transcription	Fetal Brain Female	brain
2	chr1:184504200-184522600	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr1:184505800-184524000	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr1:184505800-184530800	Weak transcription	Rectal Smooth Muscle	rectum
5	chr1:184505800-184531600	Weak transcription	Fetal Stomach	stomach
6	chr1:184511400-184530400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr1:184511800-184524600	Weak transcription	Colon Smooth Muscle	Colon
8	chr1:184512200-184524200	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr1:184512200-184524400	Weak transcription	Fetal Muscle Leg	muscle
10	chr1:184512200-184530200	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr1:184512200-184543600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr1:184512400-184530200	Weak transcription	Stomach Smooth Muscle	stomach
13	chr1:184514400-184543800	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr1:184515200-184524000	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr1:184515200-184531200	Weak transcription	NHLF	lung
16	chr1:184516000-184524200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr1:184516200-184524400	Weak transcription	Fetal Muscle Trunk	muscle
18	chr1:184516400-184522800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr1:184516400-184523000	Weak transcription	HMEC	breast
20	chr1:184516400-184524400	Weak transcription	Adipose Nuclei	Adipose
21	chr1:184516400-184524600	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr1:184516400-184529000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr1:184517000-184524200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
24	chr1:184517200-184522600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr1:184517200-184522800	Weak transcription	NHEK	skin
26	chr1:184517200-184524400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr1:184517200-184524400	Weak transcription	Left Ventricle	heart
28	chr1:184517400-184524200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr1:184517400-184524400	Weak transcription	Right Ventricle	heart
30	chr1:184517600-184522600	Weak transcription	Esophagus	oesophagus
31	chr1:184519800-184521600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr1:184519800-184521800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr1:184520200-184520800	Enhancers	HUES64 Cell Line	embryonic stem cell
34	chr1:184520200-184521000	Enhancers	Primary hematopoietic stem cells	blood
35	chr1:184520200-184521000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr1:184520400-184520800	Enhancers	HSMMtube	muscle
37	chr1:184520400-184521000	Enhancers	Primary hematopoietic stem cells short term culture	blood
38	chr1:184520400-184521200	Enhancers	iPS-15b Cell Line	embryonic stem cell
39	chr1:184520600-184520800	Enhancers	HUES48 Cell Line	embryonic stem cell
40	chr1:184520600-184520800	Enhancers	Ovary	ovary
41	chr1:184520600-184521000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr1:184520600-184521000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr1:184520600-184521000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr1:184520600-184521000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
45	chr1:184520600-184521000	Enhancers	Psoas Muscle	Psoas

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