Variant report

Variant	rs7671609
Chromosome Location	chr4:87901580-87901581
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:87854810..87857706-chr4:87898102..87901903,3	MCF-7	breast:
2	chr4:87891928..87895544-chr4:87897508..87902479,6	K562	blood:

Variant related genes	Relation type
ENSG00000172493	Chromatin interaction
ENSG00000163633	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs11930536	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11937587	1.00[AMR][1000 genomes]
rs11939722	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11943683	0.88[YRI][hapmap];1.00[AMR][1000 genomes]
rs11944829	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11945169	0.93[YRI][hapmap];1.00[AMR][1000 genomes]
rs11947276	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17012253	0.86[YRI][hapmap];0.81[AFR][1000 genomes]
rs17012255	0.81[AFR][1000 genomes]
rs17012288	1.00[AMR][1000 genomes]
rs28567446	1.00[AMR][1000 genomes]
rs6810606	0.86[YRI][hapmap]
rs6810840	0.82[YRI][hapmap]
rs6827682	0.86[YRI][hapmap]
rs6831823	0.93[YRI][hapmap];1.00[AMR][1000 genomes]
rs6833094	0.94[YRI][hapmap];1.00[AMR][1000 genomes]
rs6850907	1.00[AMR][1000 genomes]
rs6856436	1.00[AMR][1000 genomes]
rs6857010	0.94[YRI][hapmap];1.00[AMR][1000 genomes]
rs7659431	1.00[AMR][1000 genomes]
rs7676368	1.00[AMR][1000 genomes]
rs7676669	1.00[AMR][1000 genomes]
rs7677039	0.93[YRI][hapmap];1.00[AMR][1000 genomes]
rs7677287	0.94[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7690864	0.82[YRI][hapmap];1.00[AMR][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	nsv1009937	chr4:87795314-88008345	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
2	nsv999176	chr4:87869996-88098136	Strong transcription Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Genic enhancers 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 target site	27 gene(s)	inside rSNPs	diseases
3	nsv998335	chr4:87869996-88104414	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv1001017	chr4:87872160-88087003	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
5	nsv537166	chr4:87872160-88087003	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
6	nsv999098	chr4:87899091-88016048	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Strong transcription 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	25 gene(s)	inside rSNPs	diseases
7	nsv537167	chr4:87899091-88016048	Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:87872600-87926200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr4:87882600-87920200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr4:87882800-87912400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr4:87892200-87907000	Weak transcription	Brain Anterior Caudate	brain
5	chr4:87892400-87920600	Weak transcription	Stomach Smooth Muscle	stomach
6	chr4:87892800-87909400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr4:87894400-87911000	Weak transcription	Pancreas	Pancrea
8	chr4:87894600-87904200	Weak transcription	Primary T cells fromperipheralblood	blood
9	chr4:87894600-87915600	Weak transcription	Lung	lung
10	chr4:87894600-87921000	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr4:87895200-87909400	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr4:87895400-87920000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr4:87896200-87902800	Weak transcription	Primary T cells from cord blood	blood
14	chr4:87896200-87916000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr4:87896200-87919200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
16	chr4:87896400-87902800	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr4:87896800-87918800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr4:87897200-87902600	Weak transcription	Monocytes-CD14+_RO01746	blood
19	chr4:87897600-87915600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr4:87897800-87903000	Weak transcription	Primary neutrophils fromperipheralblood	blood
21	chr4:87898000-87903000	Weak transcription	Thymus	Thymus
22	chr4:87898200-87915400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr4:87898600-87901600	Enhancers	Primary B cells from peripheral blood	blood
24	chr4:87898600-87902800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
25	chr4:87898800-87902800	Weak transcription	Brain Hippocampus Middle	brain
26	chr4:87899000-87902800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr4:87899000-87902800	Weak transcription	Primary T helper cells fromperipheralblood	blood
28	chr4:87899000-87915400	Weak transcription	HUES6 Cell Line	embryonic stem cell
29	chr4:87899000-87915400	Weak transcription	Left Ventricle	heart
30	chr4:87899000-87920600	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr4:87899000-87921200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr4:87899200-87902000	Weak transcription	Gastric	stomach
33	chr4:87899200-87902200	Weak transcription	Fetal Thymus	thymus
34	chr4:87899200-87902200	Weak transcription	Spleen	Spleen
35	chr4:87899200-87902400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
36	chr4:87899200-87902400	Weak transcription	Dnd41	blood
37	chr4:87899200-87902600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
38	chr4:87899200-87902600	Weak transcription	Sigmoid Colon	Sigmoid Colon
39	chr4:87899200-87902800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr4:87899200-87902800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
41	chr4:87899200-87902800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr4:87899200-87903000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
43	chr4:87899200-87903000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
44	chr4:87899200-87903200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr4:87899200-87903400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr4:87899200-87905000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr4:87899200-87905400	Weak transcription	Colon Smooth Muscle	Colon
48	chr4:87899200-87911000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
49	chr4:87899200-87913200	Weak transcription	Liver	Liver
50	chr4:87899200-87920800	Weak transcription	Breast Myoepithelial Primary Cells	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links