Variant report

Variant	rs16845250
Chromosome Location	chr1:225946690-225946691
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:225945507..225952186-chr1:225952608..225958481,10	MCF-7	breast:
2	chr1:225942220..225946918-chr1:225947468..225951068,4	K562	blood:
3	chr1:225839653..225842222-chr1:225946045..225947653,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000154380	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs16845207	1.00[EUR][1000 genomes]
rs16845221	1.00[CEU][hapmap];0.90[GIH][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs16845230	0.85[EUR][1000 genomes]
rs2077840	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes]
rs2840964	1.00[JPT][hapmap]
rs56052403	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74148698	0.81[ASN][1000 genomes]
rs74148699	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832736	chr1:225815717-225968619	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
2	esv1795046	chr1:225874059-226091150	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers 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 miRNA target site	40 gene(s)	inside rSNPs	diseases
3	esv1834932	chr1:225874059-226091150	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
4	esv1834948	chr1:225874059-226214882	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16845250	RASIP1	trans	lymphoblastoid	seeQTL

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:225935000-225949600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr1:225939200-225949600	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr1:225943400-225949400	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr1:225943400-225949800	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr1:225943400-225951800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr1:225943600-225949800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr1:225943600-225951400	Weak transcription	Pancreas	Pancrea
8	chr1:225943600-225951800	Weak transcription	Gastric	stomach
9	chr1:225943600-225954800	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr1:225943800-225948400	Weak transcription	Primary hematopoietic stem cells	blood
11	chr1:225943800-225949800	Weak transcription	Stomach Smooth Muscle	stomach
12	chr1:225943800-225951200	Weak transcription	Brain Hippocampus Middle	brain
13	chr1:225944000-225949400	Weak transcription	A549	lung
14	chr1:225944000-225949600	Weak transcription	Right Atrium	heart
15	chr1:225944200-225949200	Weak transcription	NH-A	brain
16	chr1:225944200-225949400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr1:225944200-225949400	Weak transcription	NHLF	lung
18	chr1:225944200-225949600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr1:225944200-225949600	Weak transcription	HSMM	muscle
20	chr1:225944200-225951800	Weak transcription	Right Ventricle	heart
21	chr1:225944400-225948200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr1:225944400-225949200	Weak transcription	Osteobl	bone
23	chr1:225944400-225949400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr1:225944400-225949600	Weak transcription	Left Ventricle	heart
25	chr1:225944800-225948600	Weak transcription	HepG2	liver
26	chr1:225945600-225949800	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr1:225945800-225947000	Enhancers	Fetal Lung	lung
28	chr1:225946000-225947000	Enhancers	Adipose Nuclei	Adipose
29	chr1:225946000-225949800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
30	chr1:225946000-225949800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr1:225946200-225948800	Weak transcription	NHDF-Ad	bronchial
32	chr1:225946200-225949400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr1:225946200-225949800	Weak transcription	Muscle Satellite Cultured Cells	--
34	chr1:225946200-225949800	Weak transcription	Fetal Intestine Small	intestine
35	chr1:225946200-225959800	Weak transcription	Duodenum Mucosa	Duodenum
36	chr1:225946400-225949600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr1:225946600-225949600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr1:225946600-225949600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr1:225946600-225949600	Weak transcription	Fetal Muscle Leg	muscle
40	chr1:225946600-225949600	Weak transcription	Fetal Thymus	thymus
41	chr1:225946600-225949600	Weak transcription	Ovary	ovary
42	chr1:225946600-225950200	Weak transcription	Skeletal Muscle Male	skeletal muscle
43	chr1:225946600-225951200	Weak transcription	Lung	lung
44	chr1:225946600-225951200	Weak transcription	Spleen	Spleen
45	chr1:225946600-225955400	Weak transcription	Fetal Intestine Large	intestine

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links