Variant report

Variant	rs7513091
Chromosome Location	chr1:184488963-184488964
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	chr1:184487281..184489460-chr1:184493042..184495874,2	MCF-7	breast:

Extended variants
information (count: 38 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10399817	0.94[CHB][hapmap];0.82[GIH][hapmap]
rs10489729	0.84[CHD][hapmap];0.82[ASN][1000 genomes]
rs10911610	0.94[CHB][hapmap];0.86[ASN][1000 genomes]
rs11810399	0.80[CEU][hapmap]
rs12117823	0.87[CEU][hapmap];0.94[CHB][hapmap];0.96[TSI][hapmap];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12120604	0.94[CHB][hapmap];0.88[GIH][hapmap];0.85[ASN][1000 genomes]
rs12121612	0.94[CHB][hapmap]
rs12127697	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12129904	0.93[CEU][hapmap];0.94[CHB][hapmap];0.84[EUR][1000 genomes]
rs12138103	0.86[CEU][hapmap];1.00[CHB][hapmap];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12141469	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12143271	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1535132	0.87[CEU][hapmap];0.94[CHB][hapmap];0.84[EUR][1000 genomes]
rs16823195	0.94[CHB][hapmap];0.88[GIH][hapmap];0.83[ASN][1000 genomes]
rs16823197	0.87[CEU][hapmap];0.94[CHB][hapmap];1.00[GIH][hapmap];0.96[TSI][hapmap];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs16823238	0.94[CHB][hapmap];0.88[GIH][hapmap]
rs16823311	0.81[ASN][1000 genomes]
rs16823313	0.85[CHB][hapmap];0.84[CHD][hapmap];0.81[ASN][1000 genomes]
rs16823318	0.80[CHB][hapmap];0.81[CHD][hapmap]
rs1969683	0.81[ASN][1000 genomes]
rs2180072	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[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];0.93[TSI][hapmap];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35682339	0.89[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs58231072	0.83[ASN][1000 genomes]
rs61643431	0.82[ASN][1000 genomes]
rs61825202	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61825204	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61825205	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6659261	0.94[CHB][hapmap];0.93[CHD][hapmap];0.87[GIH][hapmap];0.84[JPT][hapmap];0.85[ASN][1000 genomes]
rs6669940	0.81[ASN][1000 genomes]
rs6683932	0.94[CHB][hapmap];0.93[CHD][hapmap];0.88[GIH][hapmap];0.84[JPT][hapmap];0.84[MKK][hapmap];0.85[ASN][1000 genomes]
rs6693408	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	0.85[ASN][1000 genomes]
rs7530615	0.81[ASN][1000 genomes]
rs7548188	0.85[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
rs7513091	MR1	cis	cerebellum	SCAN
rs7513091	TDRD5	cis	parietal	SCAN

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:184456400-184502200	Weak transcription	Fetal Muscle Trunk	muscle
2	chr1:184461600-184502800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr1:184473600-184489400	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr1:184474400-184505400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr1:184476800-184489800	Weak transcription	Fetal Stomach	stomach
6	chr1:184477400-184489000	Weak transcription	Stomach Smooth Muscle	stomach
7	chr1:184477400-184494800	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr1:184477400-184502200	Weak transcription	Primary hematopoietic stem cells	blood
9	chr1:184477800-184489200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr1:184477800-184491800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr1:184478000-184493200	Weak transcription	HSMM	muscle
12	chr1:184478400-184505200	Weak transcription	Fetal Intestine Small	intestine
13	chr1:184478600-184501200	Weak transcription	Fetal Heart	heart
14	chr1:184478800-184502200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr1:184479200-184493800	Weak transcription	Ovary	ovary
16	chr1:184479400-184489000	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr1:184480000-184495000	Weak transcription	Rectal Smooth Muscle	rectum
18	chr1:184480200-184489200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr1:184480200-184505200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr1:184480600-184501400	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr1:184481400-184504000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr1:184482000-184489600	Weak transcription	Fetal Muscle Leg	muscle
23	chr1:184482800-184489400	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr1:184483200-184489400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr1:184483400-184489200	Weak transcription	HUES64 Cell Line	embryonic stem cell
26	chr1:184483400-184492000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr1:184483400-184504000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr1:184483800-184490600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr1:184483800-184492600	Weak transcription	NHEK	skin
30	chr1:184483800-184500800	Weak transcription	Left Ventricle	heart
31	chr1:184484000-184503000	Weak transcription	NHDF-Ad	bronchial
32	chr1:184484000-184504000	Weak transcription	NHLF	lung
33	chr1:184484200-184489400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr1:184484200-184489400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr1:184485600-184489000	Enhancers	Skeletal Muscle Female	skeletal muscle
36	chr1:184485800-184504400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
37	chr1:184486800-184505400	Weak transcription	Fetal Intestine Large	intestine
38	chr1:184487000-184490000	Weak transcription	Right Atrium	heart
39	chr1:184487200-184489000	Enhancers	Fetal Brain Male	brain
40	chr1:184487800-184489800	Enhancers	iPS-15b Cell Line	embryonic stem cell
41	chr1:184488400-184489400	Weak transcription	Brain Cingulate Gyrus	brain
42	chr1:184488400-184489800	Enhancers	Small Intestine	intestine
43	chr1:184488600-184489200	Enhancers	iPS-20b Cell Line	embryonic stem cell
44	chr1:184488600-184489600	Weak transcription	Colon Smooth Muscle	Colon
45	chr1:184488600-184489800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr1:184488600-184492400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr1:184488600-184493400	Weak transcription	Muscle Satellite Cultured Cells	--
48	chr1:184488800-184496000	Weak transcription	Psoas Muscle	Psoas
49	chr1:184488800-184496000	Weak transcription	Skeletal Muscle Male	skeletal muscle

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