Variant report

Variant	rs2850354
Chromosome Location	chr4:102208664-102208665
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:102206850..102209343-chr4:102209669..102211406,2	MCF-7	breast:
2	chr4:102199385..102202283-chr4:102207975..102210015,2	MCF-7	breast:
3	chr4:102206153..102209881-chr4:102222002..102225867,4	MCF-7	breast:

Extended variants
information (count: 55 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs1031033	0.91[JPT][hapmap]
rs1031034	0.91[JPT][hapmap]
rs13123962	0.82[JPT][hapmap]
rs1348161	0.91[JPT][hapmap]
rs1441433	1.00[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1530259	0.91[JPT][hapmap]
rs1561719	0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2028475	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2099813	0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2583389	0.87[JPT][hapmap]
rs2583392	0.87[JPT][hapmap]
rs2583394	0.91[JPT][hapmap]
rs2583395	0.91[JPT][hapmap]
rs2583398	0.91[JPT][hapmap]
rs2583399	0.91[JPT][hapmap]
rs2583400	0.92[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2583401	0.92[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2583402	1.00[CEU][hapmap];0.87[CHB][hapmap];0.91[JPT][hapmap];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2583406	0.92[CEU][hapmap];0.87[CHB][hapmap];0.91[JPT][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2583410	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2850326	0.87[JPT][hapmap]
rs2850332	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2850339	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2850344	0.92[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2850348	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2850349	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2850350	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]
rs2850351	0.92[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2850352	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2850355	0.90[CEU][hapmap];0.95[JPT][hapmap];0.97[EUR][1000 genomes]
rs2850356	0.92[CEU][hapmap];0.95[JPT][hapmap];0.96[EUR][1000 genomes]
rs2850357	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2850358	0.96[EUR][1000 genomes]
rs2850360	0.92[EUR][1000 genomes]
rs2850367	0.87[JPT][hapmap]
rs2850370	0.91[JPT][hapmap]
rs2850371	0.91[JPT][hapmap]
rs2850954	0.95[EUR][1000 genomes]
rs2850963	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2850967	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2850969	0.92[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2850974	0.91[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2850975	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2850976	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs755961	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs920559	0.91[CEU][hapmap];0.95[JPT][hapmap];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs920560	0.97[EUR][1000 genomes]
rs962384	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]

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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2850354	AP001816.1	cis	Whole Blood	GTEx

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:102199600-102210400	Enhancers	iPS-18 Cell Line	embryonic stem cell
2	chr4:102200000-102211800	Weak transcription	HMEC	breast
3	chr4:102200600-102211800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr4:102200800-102209000	Weak transcription	Aorta	Aorta
5	chr4:102201000-102213000	Weak transcription	Fetal Heart	heart
6	chr4:102201200-102218200	Weak transcription	NHEK	skin
7	chr4:102201400-102214200	Weak transcription	Brain Cingulate Gyrus	brain
8	chr4:102202200-102210600	Enhancers	HUES48 Cell Line	embryonic stem cell
9	chr4:102202400-102209200	Weak transcription	Brain Substantia Nigra	brain
10	chr4:102203400-102208800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr4:102203800-102209200	Weak transcription	Primary T cells fromperipheralblood	blood
12	chr4:102203800-102209400	Weak transcription	Brain Angular Gyrus	brain
13	chr4:102204000-102208800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
14	chr4:102204000-102209600	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr4:102204400-102209400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr4:102204800-102211200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
17	chr4:102205000-102209200	Weak transcription	Monocytes-CD14+_RO01746	blood
18	chr4:102205000-102212600	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr4:102205200-102209000	Weak transcription	Primary B cells from peripheral blood	blood
20	chr4:102205200-102210600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr4:102205600-102209200	Weak transcription	Primary monocytes fromperipheralblood	blood
22	chr4:102206000-102208800	Weak transcription	Primary neutrophils fromperipheralblood	blood
23	chr4:102206200-102208800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
24	chr4:102206200-102209000	Weak transcription	Primary T helper cells PMA-I stimulated	--
25	chr4:102206200-102210200	Enhancers	Ovary	ovary
26	chr4:102206200-102210200	Enhancers	Psoas Muscle	Psoas
27	chr4:102206400-102208800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr4:102206400-102209000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr4:102206400-102209200	Weak transcription	Primary B cells from cord blood	blood
30	chr4:102206400-102209400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr4:102206600-102210600	Enhancers	iPS-15b Cell Line	embryonic stem cell
32	chr4:102206800-102210400	Enhancers	iPS-20b Cell Line	embryonic stem cell
33	chr4:102207000-102208800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr4:102207000-102209200	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr4:102207000-102216600	Weak transcription	NH-A	brain
36	chr4:102207200-102209000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr4:102207200-102209200	Weak transcription	Muscle Satellite Cultured Cells	--
38	chr4:102207200-102210000	Weak transcription	HUVEC	blood vessel
39	chr4:102207200-102212000	Weak transcription	Duodenum Mucosa	Duodenum
40	chr4:102207400-102209000	Weak transcription	Right Atrium	heart
41	chr4:102207400-102209800	Weak transcription	NHDF-Ad	bronchial
42	chr4:102207400-102209800	Weak transcription	Osteobl	bone
43	chr4:102207400-102212000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr4:102207400-102212000	Weak transcription	Gastric	stomach
45	chr4:102207400-102214200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr4:102207400-102214200	Weak transcription	Esophagus	oesophagus
47	chr4:102207600-102208800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr4:102207600-102209600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr4:102207600-102211400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
50	chr4:102207600-102226400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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