Variant report

Variant	rs1171812
Chromosome Location	chr10:61655297-61655298
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:61620903..61623071-chr10:61654123..61657104,2	MCF-7	breast:
2	chr10:61612125..61614506-chr10:61653727..61655792,2	MCF-7	breast:
3	chr10:61629487..61632652-chr10:61653201..61655969,3	K562	blood:
4	chr10:61629487..61631429-chr10:61653201..61655597,2	K562	blood:
5	chr10:61654182..61656949-chr10:61658544..61661969,6	MCF-7	breast:

Extended variants
information (count: 8 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs1171814	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1171830	0.85[CEU][hapmap];0.91[CHB][hapmap];0.83[GIH][hapmap];0.84[MEX][hapmap]
rs1171832	0.81[AMR][1000 genomes]
rs1626088	0.82[GIH][hapmap];0.91[JPT][hapmap]
rs1664256	0.87[GIH][hapmap]
rs1684901	0.89[CEU][hapmap];0.89[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1795420	chr10:61637271-61669227	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
2	esv1800316	chr10:61639599-61700473	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1171812	EGR2	cis	parietal	SCAN

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:61625000-61655400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr10:61641600-61664200	Weak transcription	A549	lung
3	chr10:61641800-61655400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr10:61643000-61659400	Weak transcription	Hela-S3	cervix
5	chr10:61645800-61659400	Weak transcription	Fetal Brain Male	brain
6	chr10:61647200-61655400	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr10:61648600-61657600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr10:61649800-61664200	Weak transcription	Placenta	Placenta
9	chr10:61650000-61659600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr10:61650000-61659800	Weak transcription	Thymus	Thymus
11	chr10:61650200-61658000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr10:61650200-61659400	Weak transcription	Fetal Thymus	thymus
13	chr10:61650200-61664000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr10:61650200-61664200	Weak transcription	Fetal Muscle Trunk	muscle
15	chr10:61650400-61659600	Weak transcription	Dnd41	blood
16	chr10:61650800-61656200	Enhancers	Breast Myoepithelial Primary Cells	Breast
17	chr10:61651000-61656400	Enhancers	Brain Hippocampus Middle	brain
18	chr10:61651000-61656800	Enhancers	Cortex derived primary cultured neurospheres	brain
19	chr10:61651200-61655400	Enhancers	K562	blood
20	chr10:61651200-61656200	Enhancers	Left Ventricle	heart
21	chr10:61651200-61656200	Enhancers	Pancreas	Pancrea
22	chr10:61651200-61656200	Enhancers	Sigmoid Colon	Sigmoid Colon
23	chr10:61651200-61656200	Enhancers	Skeletal Muscle Female	skeletal muscle
24	chr10:61651200-61656200	Enhancers	Small Intestine	intestine
25	chr10:61651200-61656400	Enhancers	Brain Anterior Caudate	brain
26	chr10:61651200-61656400	Enhancers	Brain Substantia Nigra	brain
27	chr10:61651200-61656600	Enhancers	NHEK	skin
28	chr10:61651200-61662000	Enhancers	Stomach Mucosa	stomach
29	chr10:61651200-61663400	Enhancers	Colon Smooth Muscle	Colon
30	chr10:61651400-61656400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr10:61651400-61664000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr10:61651600-61656200	Enhancers	Esophagus	oesophagus
33	chr10:61651600-61657800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
34	chr10:61651800-61656200	Enhancers	Skeletal Muscle Male	skeletal muscle
35	chr10:61651800-61662000	Enhancers	Rectal Smooth Muscle	rectum
36	chr10:61652000-61659200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr10:61653000-61656200	Enhancers	Gastric	stomach
38	chr10:61653000-61656400	Enhancers	Brain Angular Gyrus	brain
39	chr10:61653200-61656200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr10:61653200-61656200	Enhancers	Placenta Amnion	Placenta Amnion
41	chr10:61653200-61656200	Enhancers	HMEC	breast
42	chr10:61653200-61657000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr10:61653200-61657600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
44	chr10:61653200-61658000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr10:61653200-61658200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
46	chr10:61653200-61658200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr10:61653400-61655600	Weak transcription	Primary B cells from cord blood	blood
48	chr10:61653400-61656800	Enhancers	Rectal Mucosa Donor 29	rectum
49	chr10:61653400-61657600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr10:61653400-61660000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links