Variant report

Variant	rs2850348
Chromosome Location	chr4:102201704-102201705
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:102199385..102202283-chr4:102207975..102210015,2	MCF-7	breast:
2	chr4:102191153..102193723-chr4:102199346..102202643,3	MCF-7	breast:
3	chr4:102195298..102197332-chr4:102200967..102203266,2	MCF-7	breast:

Extended variants
information (count: 39 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1441433	0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1561719	0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2028475	0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2099813	0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2583400	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2583401	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2583402	0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2583406	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2583410	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2850332	0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2850339	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2850344	0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2850349	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2850350	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2850351	0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2850352	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2850354	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2850355	0.98[EUR][1000 genomes]
rs2850356	0.97[EUR][1000 genomes]
rs2850357	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2850358	0.97[EUR][1000 genomes]
rs2850360	0.92[EUR][1000 genomes]
rs2850954	0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2850963	0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2850967	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2850969	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2850974	0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2850975	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2850976	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs755961	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs920559	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs920560	0.98[EUR][1000 genomes]
rs962384	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2850348	AP001816.1	cis	Whole Blood	GTEx

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:102180600-102203000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr4:102184000-102203200	Weak transcription	Primary hematopoietic stem cells	blood
3	chr4:102188800-102203200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr4:102191400-102202200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
5	chr4:102192800-102208600	Weak transcription	Fetal Kidney	kidney
6	chr4:102193000-102203400	Weak transcription	Brain Angular Gyrus	brain
7	chr4:102193800-102201800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr4:102194000-102205200	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr4:102194200-102203000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr4:102195400-102203400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr4:102196600-102203000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr4:102197200-102202200	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr4:102197400-102203600	Weak transcription	Left Ventricle	heart
14	chr4:102197400-102203600	Weak transcription	Pancreas	Pancrea
15	chr4:102198400-102206800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr4:102198600-102203400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr4:102198800-102203200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr4:102198800-102207800	Enhancers	HUES64 Cell Line	embryonic stem cell
19	chr4:102199600-102203600	Weak transcription	Small Intestine	intestine
20	chr4:102199600-102205200	Enhancers	Primary B cells from peripheral blood	blood
21	chr4:102199600-102210400	Enhancers	iPS-18 Cell Line	embryonic stem cell
22	chr4:102199800-102202400	Weak transcription	Primary T cells from cord blood	blood
23	chr4:102199800-102203000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
24	chr4:102199800-102206800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr4:102200000-102211800	Weak transcription	HMEC	breast
26	chr4:102200200-102206200	Enhancers	iPS-15b Cell Line	embryonic stem cell
27	chr4:102200400-102201800	Enhancers	Primary monocytes fromperipheralblood	blood
28	chr4:102200400-102202600	Enhancers	Primary hematopoietic stem cells short term culture	blood
29	chr4:102200600-102202000	Weak transcription	Brain Substantia Nigra	brain
30	chr4:102200600-102203000	Weak transcription	Primary T helper cells fromperipheralblood	blood
31	chr4:102200600-102211800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr4:102200800-102202200	Weak transcription	Brain Hippocampus Middle	brain
33	chr4:102200800-102202400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr4:102200800-102204400	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr4:102200800-102206200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr4:102200800-102206200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr4:102200800-102209000	Weak transcription	Aorta	Aorta
38	chr4:102201000-102202000	Weak transcription	Colon Smooth Muscle	Colon
39	chr4:102201000-102202200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
40	chr4:102201000-102202200	Weak transcription	H9 Cell Line	embryonic stem cell
41	chr4:102201000-102202200	Weak transcription	HUES48 Cell Line	embryonic stem cell
42	chr4:102201000-102203200	Weak transcription	Primary T helper cells PMA-I stimulated	--
43	chr4:102201000-102203400	Weak transcription	Psoas Muscle	Psoas
44	chr4:102201000-102203400	Weak transcription	Right Atrium	heart
45	chr4:102201000-102203600	Weak transcription	Fetal Thymus	thymus
46	chr4:102201000-102203600	Weak transcription	Sigmoid Colon	Sigmoid Colon
47	chr4:102201000-102206200	Weak transcription	Ovary	ovary
48	chr4:102201000-102206800	Weak transcription	Gastric	stomach
49	chr4:102201000-102207000	Weak transcription	Skeletal Muscle Male	skeletal muscle
50	chr4:102201000-102213000	Weak transcription	Fetal Heart	heart

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