Variant report

Variant	rs789709
Chromosome Location	chr12:64471307-64471308
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:64466604..64468204-chr12:64469999..64471636,2	MCF-7	breast:
2	chr12:64464103..64466762-chr12:64471161..64473294,2	MCF-7	breast:

Extended variants
information (count: 9 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs11175239	0.87[CHB][hapmap]
rs11175240	0.87[CHB][hapmap]
rs1456042	0.93[CHB][hapmap];0.82[JPT][hapmap];0.86[YRI][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1827074	0.84[EUR][1000 genomes]
rs4436640	0.87[CHB][hapmap];0.81[YRI][hapmap]
rs57477949	0.86[EUR][1000 genomes]
rs717001	0.87[CHB][hapmap]
rs789743	0.92[CEU][hapmap];0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3351487	chr12:64420364-64763950	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs789709	SRGAP1	cis	Esophagus Muscularis	GTEx

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:64433600-64474200	Weak transcription	Left Ventricle	heart
2	chr12:64434000-64481600	Weak transcription	HUVEC	blood vessel
3	chr12:64436600-64474200	Weak transcription	Rectal Smooth Muscle	rectum
4	chr12:64436800-64474200	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr12:64440000-64479200	Weak transcription	Esophagus	oesophagus
6	chr12:64441000-64475000	Weak transcription	Hela-S3	cervix
7	chr12:64445200-64474200	Weak transcription	Fetal Lung	lung
8	chr12:64451200-64476600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr12:64453000-64476600	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr12:64453600-64472800	Weak transcription	Brain Anterior Caudate	brain
11	chr12:64453800-64473600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr12:64453800-64476600	Weak transcription	Brain Substantia Nigra	brain
13	chr12:64454800-64476600	Weak transcription	Brain Hippocampus Middle	brain
14	chr12:64455000-64474200	Weak transcription	Colon Smooth Muscle	Colon
15	chr12:64455200-64481600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr12:64457000-64510600	Weak transcription	HepG2	liver
17	chr12:64457600-64472600	Weak transcription	Lung	lung
18	chr12:64457800-64474000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr12:64457800-64474400	Weak transcription	Small Intestine	intestine
20	chr12:64459000-64472600	Weak transcription	Fetal Intestine Large	intestine
21	chr12:64459000-64472600	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr12:64459000-64474000	Weak transcription	Ovary	ovary
23	chr12:64459000-64476600	Weak transcription	Brain Cingulate Gyrus	brain
24	chr12:64459000-64479800	Weak transcription	Gastric	stomach
25	chr12:64459200-64474200	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr12:64460200-64472800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr12:64460200-64474000	Weak transcription	Rectal Mucosa Donor 29	rectum
28	chr12:64460200-64476600	Weak transcription	Brain Germinal Matrix	brain
29	chr12:64460200-64476800	Weak transcription	Fetal Kidney	kidney
30	chr12:64460800-64473600	Weak transcription	HMEC	breast
31	chr12:64460800-64476600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr12:64461000-64474400	Weak transcription	Stomach Smooth Muscle	stomach
33	chr12:64461800-64471800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr12:64463200-64472800	Weak transcription	Cortex derived primary cultured neurospheres	brain
35	chr12:64464800-64472600	Weak transcription	HSMMtube	muscle
36	chr12:64465000-64472600	Weak transcription	Adipose Nuclei	Adipose
37	chr12:64466000-64476600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr12:64466600-64472600	Weak transcription	NHLF	lung
39	chr12:64466800-64472000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr12:64466800-64472600	Weak transcription	Fetal Muscle Leg	muscle
41	chr12:64466800-64474400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr12:64467000-64472600	Weak transcription	Fetal Brain Female	brain
43	chr12:64467000-64472600	Weak transcription	Fetal Stomach	stomach
44	chr12:64467000-64474400	Weak transcription	Duodenum Mucosa	Duodenum
45	chr12:64467000-64474400	Weak transcription	Fetal Brain Male	brain
46	chr12:64467000-64474400	Weak transcription	Pancreas	Pancrea
47	chr12:64467000-64482400	Weak transcription	Aorta	Aorta
48	chr12:64467200-64472400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
49	chr12:64467200-64472400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr12:64467200-64476800	Weak transcription	NH-A	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links