Variant report

Variant	rs1989909
Chromosome Location	chr7:27957857-27957858
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:27957341..27960196-chr7:27962479..27964875,2	K562	blood:
2	chr7:27956076..27958841-chr7:27959567..27962104,2	MCF-7	breast:

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs13224987	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17621988	1.00[CEU][hapmap];0.95[GIH][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17622746	0.81[CEU][hapmap]
rs195	0.83[CHB][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs1989908	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs202	0.91[ASW][hapmap];0.84[LWK][hapmap];0.88[MKK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs203	1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs2040666	0.81[CEU][hapmap];0.81[TSI][hapmap]
rs206	1.00[YRI][hapmap];0.93[AFR][1000 genomes]
rs209	1.00[ASW][hapmap];0.88[CHD][hapmap];0.86[LWK][hapmap];0.95[MKK][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs210	0.81[YRI][hapmap]
rs212	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[CHD][hapmap];0.94[JPT][hapmap];0.91[LWK][hapmap];0.80[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34634838	0.91[EUR][1000 genomes]
rs3919460	0.81[CEU][hapmap]
rs4722747	0.81[CEU][hapmap]
rs7776540	0.87[CEU][hapmap];0.81[GIH][hapmap];0.84[TSI][hapmap]
rs7783465	0.81[CEU][hapmap]

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	nsv949025	chr7:27578167-28075172	Active TSS Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	esv2758109	chr7:27793616-27972869	Weak transcription Genic enhancers Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
3	esv2759520	chr7:27793616-27972869	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
4	nsv1030685	chr7:27844038-28177301	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
5	nsv1024819	chr7:27949955-28020969	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv520555	chr7:27952629-27958750	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1989909	HOXA10	cis	cerebellum	SCAN

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:27941400-27990800	Weak transcription	Primary T cells from cord blood	blood
2	chr7:27941600-27962800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr7:27942400-28005600	Weak transcription	Primary monocytes fromperipheralblood	blood
4	chr7:27950400-27963000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr7:27950800-27958200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr7:27951400-27963000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr7:27952600-27959000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr7:27952600-27960200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr7:27953600-27959400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr7:27954200-27959600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr7:27954400-27959600	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr7:27954600-27962600	Weak transcription	Right Ventricle	heart
13	chr7:27954600-27963000	Weak transcription	Left Ventricle	heart
14	chr7:27955200-27958400	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr7:27955200-27962600	Weak transcription	Fetal Muscle Trunk	muscle
16	chr7:27955800-27960800	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr7:27956000-27958000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr7:27956000-27958000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr7:27956000-27958400	Enhancers	NHEK	skin
20	chr7:27956400-27960800	Weak transcription	Brain Hippocampus Middle	brain
21	chr7:27956400-27961000	Enhancers	HUVEC	blood vessel
22	chr7:27956600-27958000	Enhancers	Colon Smooth Muscle	Colon
23	chr7:27956600-27979800	Weak transcription	Aorta	Aorta
24	chr7:27956800-27958000	Enhancers	Rectal Smooth Muscle	rectum
25	chr7:27956800-27960600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr7:27957000-27958200	Flanking Active TSS	A549	lung
27	chr7:27957000-27958400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr7:27957000-27958400	Enhancers	Osteobl	bone
29	chr7:27957000-27958600	Enhancers	Fetal Heart	heart
30	chr7:27957000-27962800	Weak transcription	Primary B cells from cord blood	blood
31	chr7:27957200-27958000	Enhancers	Muscle Satellite Cultured Cells	--
32	chr7:27957200-27958000	Enhancers	Stomach Mucosa	stomach
33	chr7:27957200-27958000	Enhancers	NHDF-Ad	bronchial
34	chr7:27957200-27958200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr7:27957200-27958400	Enhancers	NH-A	brain
36	chr7:27957200-27979000	Weak transcription	Monocytes-CD14+_RO01746	blood
37	chr7:27957400-27958000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr7:27957400-27958400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr7:27957400-27958600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr7:27957400-27959200	Enhancers	Primary B cells from peripheral blood	blood
41	chr7:27957400-27960800	Weak transcription	Placenta	Placenta
42	chr7:27957400-27962600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr7:27957400-27963200	Weak transcription	Stomach Smooth Muscle	stomach
44	chr7:27957600-27958000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr7:27957600-27960000	Weak transcription	HSMM	muscle
46	chr7:27957600-27969200	Weak transcription	Duodenum Smooth Muscle	Duodenum
47	chr7:27957600-28000800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr7:27957800-27959200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr7:27957800-27960400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr7:27957800-27960600	Weak transcription	Brain Cingulate Gyrus	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links