Variant report

Variant	rs2850998
Chromosome Location	chr4:102132618-102132619
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:102131746..102133996-chr4:102142309..102145275,2	MCF-7	breast:
2	chr4:102132378..102137529-chr4:102267092..102270901,7	MCF-7	breast:
3	chr4:102129760..102133881-chr4:102266334..102270307,6	MCF-7	breast:
4	chr4:102119014..102119905-chr4:102132461..102133442,2	MCF-7	breast:
5	chr4:102130741..102132972-chr4:102224508..102226264,2	MCF-7	breast:
6	chr4:102116031..102123578-chr4:102130356..102136503,10	MCF-7	breast:

Variant related genes	Relation type
ENSG00000254531	Chromatin interaction
ENSG00000138814	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs1157038	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11934140	0.83[YRI][hapmap]
rs11941610	0.87[YRI][hapmap]
rs1395474	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1395475	0.90[CEU][hapmap]
rs1472825	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1506800	0.90[CEU][hapmap]
rs2135608	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2135609	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2135612	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2659508	0.89[CEU][hapmap]
rs2659511	0.82[CEU][hapmap]
rs2659512	0.90[CEU][hapmap]
rs2659513	0.90[CEU][hapmap]
rs2659516	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2659517	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2659518	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2659519	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2659520	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2659521	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2659522	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2659523	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2659525	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2659527	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2659529	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2659530	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2659531	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2659533	0.89[CEU][hapmap]
rs2659534	0.89[CEU][hapmap]
rs2659538	0.89[CEU][hapmap]
rs2659541	0.90[CEU][hapmap]
rs2850347	0.89[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2850365	0.89[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2850373	0.88[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2850951	0.89[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2850972	0.88[CEU][hapmap];0.90[JPT][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2850985	0.82[CEU][hapmap]
rs2850987	0.90[CEU][hapmap]
rs2850989	1.00[CEU][hapmap]
rs2850994	0.89[CEU][hapmap]
rs2850996	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2850999	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2851001	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2851002	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2851003	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2851009	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3789748	0.80[YRI][hapmap]
rs3804366	0.89[CEU][hapmap]
rs3804381	0.84[YRI][hapmap]
rs3804408	0.83[YRI][hapmap]
rs67445056	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs713455	0.83[YRI][hapmap]
rs958379	0.87[YRI][hapmap]
rs970071	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[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

No data

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:102123200-102133400	Weak transcription	Psoas Muscle	Psoas
2	chr4:102123200-102133400	Weak transcription	Right Atrium	heart
3	chr4:102123400-102132800	Weak transcription	Primary neutrophils fromperipheralblood	blood
4	chr4:102124200-102132800	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr4:102128000-102138200	Weak transcription	Primary B cells from cord blood	blood
6	chr4:102129000-102140400	Weak transcription	Primary T helper cells PMA-I stimulated	--
7	chr4:102129600-102135600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr4:102129600-102138600	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr4:102131200-102133400	Enhancers	iPS-18 Cell Line	embryonic stem cell
10	chr4:102131400-102133200	Enhancers	HUES6 Cell Line	embryonic stem cell
11	chr4:102131600-102133000	Enhancers	Small Intestine	intestine
12	chr4:102131600-102133600	Enhancers	Muscle Satellite Cultured Cells	--
13	chr4:102131800-102132800	Active TSS	A549	lung
14	chr4:102131800-102133000	Enhancers	HUES64 Cell Line	embryonic stem cell
15	chr4:102131800-102133000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr4:102131800-102146000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr4:102132000-102133000	Enhancers	NH-A	brain
18	chr4:102132000-102133200	Enhancers	HUES48 Cell Line	embryonic stem cell
19	chr4:102132000-102133200	Enhancers	iPS-15b Cell Line	embryonic stem cell
20	chr4:102132200-102132800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
21	chr4:102132200-102133000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr4:102132200-102133000	Enhancers	HMEC	breast
23	chr4:102132200-102133000	Enhancers	NHDF-Ad	bronchial
24	chr4:102132200-102133200	Enhancers	HepG2	liver
25	chr4:102132200-102133200	Enhancers	HSMM	muscle
26	chr4:102132200-102133600	Enhancers	Sigmoid Colon	Sigmoid Colon
27	chr4:102132200-102133600	Enhancers	Osteobl	bone
28	chr4:102132200-102133800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr4:102132200-102133800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr4:102132400-102132800	Enhancers	iPS-20b Cell Line	embryonic stem cell
31	chr4:102132400-102132800	Enhancers	Stomach Mucosa	stomach
32	chr4:102132400-102133000	Enhancers	ES-I3 Cell Line	embryonic stem cell
33	chr4:102132400-102133000	Enhancers	NHEK	skin
34	chr4:102132400-102133200	Enhancers	Duodenum Smooth Muscle	Duodenum
35	chr4:102132400-102133600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr4:102132400-102138400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr4:102132600-102133000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr4:102132600-102133000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
39	chr4:102132600-102133000	Enhancers	Colon Smooth Muscle	Colon
40	chr4:102132600-102133200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr4:102132600-102133400	Weak transcription	H1 Cell Line	embryonic stem cell
42	chr4:102132600-102133800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin

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