Variant report

Variant	rs2850350
Chromosome Location	chr4:102205385-102205386
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	chr4:102202182..102203692-chr4:102205246..102206935,2	MCF-7	breast:

Extended variants
information (count: 90 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs10004357	0.81[JPT][hapmap]
rs10016548	0.81[JPT][hapmap]
rs1031033	0.86[JPT][hapmap]
rs1031034	0.86[JPT][hapmap]
rs10516470	0.82[JPT][hapmap]
rs11934140	0.82[JPT][hapmap]
rs11941610	0.82[JPT][hapmap]
rs13115754	0.82[JPT][hapmap]
rs13116679	0.82[JPT][hapmap]
rs13117949	0.82[JPT][hapmap];0.85[YRI][hapmap]
rs13123962	0.85[JPT][hapmap]
rs13137393	0.86[ASW][hapmap];0.82[JPT][hapmap]
rs13151505	0.82[JPT][hapmap]
rs1348161	0.86[JPT][hapmap]
rs1441433	1.00[CEU][hapmap];0.82[CHB][hapmap];0.80[GIH][hapmap];0.91[JPT][hapmap];0.83[MEX][hapmap];0.96[TSI][hapmap];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1530259	0.86[JPT][hapmap]
rs1561719	0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2028475	0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2099813	0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2165505	0.82[JPT][hapmap]
rs2583389	0.86[JPT][hapmap]
rs2583392	0.86[JPT][hapmap]
rs2583394	0.86[JPT][hapmap]
rs2583395	0.86[JPT][hapmap]
rs2583398	0.86[JPT][hapmap]
rs2583399	0.86[JPT][hapmap]
rs2583400	1.00[CEU][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2583401	1.00[CEU][hapmap];0.81[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2583402	1.00[CEU][hapmap];0.86[CHB][hapmap];0.81[CHD][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];0.84[MEX][hapmap];0.96[TSI][hapmap];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2583405	0.82[JPT][hapmap]
rs2583406	0.93[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2583407	0.82[JPT][hapmap]
rs2583410	0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2850326	0.86[JPT][hapmap]
rs2850332	1.00[CEU][hapmap];0.87[CHB][hapmap];0.83[CHD][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.96[TSI][hapmap];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2850335	0.82[JPT][hapmap]
rs2850336	0.82[JPT][hapmap]
rs2850338	0.82[JPT][hapmap]
rs2850339	0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2850344	1.00[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2850348	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2850349	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2850351	1.00[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2850352	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2850354	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2850355	0.92[CEU][hapmap];0.95[JPT][hapmap];0.99[EUR][1000 genomes]
rs2850356	0.93[CEU][hapmap];0.95[JPT][hapmap];0.98[EUR][1000 genomes]
rs2850357	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2850358	0.98[EUR][1000 genomes]
rs2850359	0.82[JPT][hapmap]
rs2850360	0.94[EUR][1000 genomes]
rs2850367	0.86[JPT][hapmap]
rs2850370	0.86[JPT][hapmap]
rs2850371	0.86[JPT][hapmap]
rs2850954	0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2850960	0.82[JPT][hapmap]
rs2850963	1.00[CEU][hapmap];0.87[CHB][hapmap];0.83[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.96[TSI][hapmap];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2850964	0.82[JPT][hapmap]
rs2850967	0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2850969	1.00[CEU][hapmap];0.95[JPT][hapmap];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2850971	0.82[JPT][hapmap]
rs2850974	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2850975	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2850976	1.00[CEU][hapmap];0.87[CHB][hapmap];0.87[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3789748	0.82[JPT][hapmap]
rs3804381	0.82[JPT][hapmap]
rs3804403	0.82[JPT][hapmap]
rs3804406	0.93[ASW][hapmap];0.82[JPT][hapmap];0.85[YRI][hapmap]
rs3804407	0.82[JPT][hapmap]
rs3804408	0.82[JPT][hapmap]
rs3804409	0.82[JPT][hapmap]
rs3804416	0.82[JPT][hapmap]
rs3804420	0.82[JPT][hapmap]
rs3827773	0.81[JPT][hapmap]
rs6854591	0.82[JPT][hapmap]
rs713455	0.82[JPT][hapmap]
rs755961	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[YRI][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs920559	0.93[CEU][hapmap];0.91[JPT][hapmap];0.84[TSI][hapmap];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs920560	0.99[EUR][1000 genomes]
rs958379	0.81[JPT][hapmap]
rs962384	0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs978373	0.82[JPT][hapmap]
rs9997767	0.82[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931418	chr4:101500167-102443207	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv999741	chr4:102009017-102454115	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
3	nsv537199	chr4:102009017-102454115	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1004766	chr4:102009017-102713765	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
5	nsv537200	chr4:102009017-102713765	Weak transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
6	nsv1011351	chr4:102056024-102450302	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
7	nsv879676	chr4:102202285-102340930	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2850350	AP001816.1	cis	Whole Blood	GTEx
rs2850350	FRAT1	trans	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:102192800-102208600	Weak transcription	Fetal Kidney	kidney
2	chr4:102198400-102206800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr4:102198800-102207800	Enhancers	HUES64 Cell Line	embryonic stem cell
4	chr4:102199600-102210400	Enhancers	iPS-18 Cell Line	embryonic stem cell
5	chr4:102199800-102206800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr4:102200000-102211800	Weak transcription	HMEC	breast
7	chr4:102200200-102206200	Enhancers	iPS-15b Cell Line	embryonic stem cell
8	chr4:102200600-102211800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr4:102200800-102206200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr4:102200800-102206200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr4:102200800-102209000	Weak transcription	Aorta	Aorta
12	chr4:102201000-102206200	Weak transcription	Ovary	ovary
13	chr4:102201000-102206800	Weak transcription	Gastric	stomach
14	chr4:102201000-102207000	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr4:102201000-102213000	Weak transcription	Fetal Heart	heart
16	chr4:102201200-102205600	Weak transcription	HUVEC	blood vessel
17	chr4:102201200-102207800	Weak transcription	Adipose Nuclei	Adipose
18	chr4:102201200-102218200	Weak transcription	NHEK	skin
19	chr4:102201400-102205400	Weak transcription	A549	lung
20	chr4:102201400-102206000	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr4:102201400-102206200	Weak transcription	NH-A	brain
22	chr4:102201400-102206800	Weak transcription	Osteobl	bone
23	chr4:102201400-102214200	Weak transcription	Brain Cingulate Gyrus	brain
24	chr4:102201600-102206000	Weak transcription	NHDF-Ad	bronchial
25	chr4:102201600-102206000	Weak transcription	NHLF	lung
26	chr4:102201600-102206200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr4:102201600-102206800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr4:102202200-102210600	Enhancers	HUES48 Cell Line	embryonic stem cell
29	chr4:102202400-102205600	Enhancers	Primary T cells from cord blood	blood
30	chr4:102202400-102205600	Weak transcription	Colon Smooth Muscle	Colon
31	chr4:102202400-102205800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr4:102202400-102209200	Weak transcription	Brain Substantia Nigra	brain
33	chr4:102202600-102208600	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr4:102202800-102206000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
35	chr4:102203000-102206000	Enhancers	Primary neutrophils fromperipheralblood	blood
36	chr4:102203000-102206200	Enhancers	Primary T helper cells fromperipheralblood	blood
37	chr4:102203000-102207800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
38	chr4:102203200-102205800	Enhancers	Primary B cells from cord blood	blood
39	chr4:102203200-102205800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr4:102203200-102206200	Enhancers	Primary hematopoietic stem cells	blood
41	chr4:102203200-102206200	Enhancers	Primary T helper cells PMA-I stimulated	--
42	chr4:102203200-102206800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
43	chr4:102203400-102205600	Enhancers	Primary monocytes fromperipheralblood	blood
44	chr4:102203400-102208800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
45	chr4:102203600-102208200	Enhancers	Stomach Mucosa	stomach
46	chr4:102203800-102206400	Enhancers	iPS-20b Cell Line	embryonic stem cell
47	chr4:102203800-102206600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr4:102203800-102209200	Weak transcription	Primary T cells fromperipheralblood	blood
49	chr4:102203800-102209400	Weak transcription	Brain Angular Gyrus	brain
50	chr4:102204000-102205600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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