Variant report

Variant	rs907872
Chromosome Location	chr2:20369948-20369949
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:20343897..20346310-chr2:20367652..20370210,2	MCF-7	breast:
2	chr2:20101674..20103205-chr2:20369213..20371363,2	MCF-7	breast:
3	chr2:20369269..20371931-chr2:20376136..20379582,4	MCF-7	breast:
4	chr2:20248476..20251356-chr2:20368246..20369984,2	MCF-7	breast:
5	chr2:20368402..20370917-chr2:20372413..20374946,2	K562	blood:
6	chr2:20368602..20370551-chr2:20379312..20381264,2	MCF-7	breast:
7	chr2:20347344..20349010-chr2:20367659..20370421,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000183891	Chromatin interaction
ENSG00000271991	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs11894335	0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2090035	0.83[CEU][hapmap];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2137718	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs907869	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009521	chr2:20310479-20388959	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv1012841	chr2:20328894-20415168	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv1004083	chr2:20336237-20388138	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv1000323	chr2:20336237-20419923	Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS 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	15 gene(s)	inside rSNPs	diseases
5	nsv1004947	chr2:20342264-20388138	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv997958	chr2:20349343-20386339	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	nsv1005524	chr2:20349343-20388138	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
8	nsv999131	chr2:20350751-20377607	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	nsv998067	chr2:20350751-20386339	Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
10	nsv1001531	chr2:20350751-20388138	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
11	nsv1007926	chr2:20350751-20393557	Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:20362400-20371400	Weak transcription	Right Atrium	heart
2	chr2:20363800-20374000	Enhancers	Breast Myoepithelial Primary Cells	Breast
3	chr2:20364400-20372000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr2:20364800-20372200	Enhancers	NHEK	skin
5	chr2:20366000-20370400	Weak transcription	Fetal Kidney	kidney
6	chr2:20366000-20370800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr2:20366000-20371200	Weak transcription	Fetal Lung	lung
8	chr2:20366400-20372000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr2:20366600-20371600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr2:20366800-20372600	Enhancers	Placenta	Placenta
11	chr2:20367200-20376600	Weak transcription	Stomach Mucosa	stomach
12	chr2:20367400-20372200	Weak transcription	GM12878-XiMat	blood
13	chr2:20367600-20371200	Weak transcription	Pancreas	Pancrea
14	chr2:20367600-20371200	Weak transcription	HMEC	breast
15	chr2:20367800-20383600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr2:20368000-20370600	Enhancers	Brain Germinal Matrix	brain
17	chr2:20368600-20370200	Enhancers	Cortex derived primary cultured neurospheres	brain
18	chr2:20368600-20370600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
19	chr2:20369000-20370000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr2:20369000-20370400	Enhancers	HUES6 Cell Line	embryonic stem cell
21	chr2:20369000-20374400	Enhancers	Esophagus	oesophagus
22	chr2:20369200-20370000	Enhancers	iPS-18 Cell Line	embryonic stem cell
23	chr2:20369200-20370200	Enhancers	H1 Cell Line	embryonic stem cell
24	chr2:20369200-20370400	Enhancers	HUES48 Cell Line	embryonic stem cell
25	chr2:20369200-20370400	Enhancers	NH-A	brain
26	chr2:20369200-20370800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr2:20369400-20370000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr2:20369400-20370000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr2:20369400-20370200	Enhancers	ES-I3 Cell Line	embryonic stem cell
30	chr2:20369400-20370200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr2:20369400-20370800	Enhancers	Spleen	Spleen
32	chr2:20369600-20370000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr2:20369600-20370200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr2:20369600-20371400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
35	chr2:20369600-20371800	Enhancers	Fetal Intestine Large	intestine
36	chr2:20369600-20377800	Weak transcription	Rectal Mucosa Donor 31	rectum
37	chr2:20369800-20370000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr2:20369800-20370000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr2:20369800-20370000	Enhancers	Brain Substantia Nigra	brain
40	chr2:20369800-20370000	Bivalent Enhancer	Fetal Muscle Leg	muscle
41	chr2:20369800-20370200	Enhancers	HUES64 Cell Line	embryonic stem cell
42	chr2:20369800-20370200	Enhancers	Brain Anterior Caudate	brain
43	chr2:20369800-20370600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr2:20369800-20370600	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr2:20369800-20370800	Enhancers	HUVEC	blood vessel
46	chr2:20369800-20371000	Enhancers	Lung	lung
47	chr2:20369800-20371800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr2:20369800-20371800	Enhancers	Fetal Intestine Small	intestine
49	chr2:20369800-20374200	Enhancers	Liver	Liver

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