Variant report

Variant	rs16955672
Chromosome Location	chr18:9807321-9807322
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr18:9613360..9615282-chr18:9806847..9809543,2	MCF-7	breast:
2	chr18:9807137..9811222-chr18:9917740..9921159,3	K562	blood:

Variant related genes	Relation type
ENSG00000263627	Chromatin interaction
ENSG00000154845	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs12454355	1.00[CEU][hapmap];1.00[MEX][hapmap]
rs2267563	1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs2867813	1.00[CEU][hapmap]
rs73385080	1.00[ASN][1000 genomes]
rs73385082	1.00[ASN][1000 genomes]

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	nsv458024	chr18:9558240-9828448	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
2	nsv576448	chr18:9558240-9828448	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
3	nsv469897	chr18:9674498-9870517	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
4	nsv482461	chr18:9674498-9870517	Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
5	nsv909366	chr18:9760942-9827368	Weak transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	12 gene(s)	inside rSNPs	diseases
6	nsv833586	chr18:9783830-9971693	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	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
rs16955672	GPHN	trans	lymphoblastoid	seeQTL

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:9771800-9807800	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr18:9783400-9808600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr18:9803600-9808200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr18:9804200-9816800	Weak transcription	Primary B cells from cord blood	blood
5	chr18:9804400-9807800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr18:9804400-9808000	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr18:9804400-9808200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr18:9804400-9808200	Weak transcription	HMEC	breast
9	chr18:9804400-9808400	Weak transcription	NHLF	lung
10	chr18:9804400-9808600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr18:9804400-9808600	Weak transcription	Psoas Muscle	Psoas
12	chr18:9804600-9807400	Weak transcription	NHEK	skin
13	chr18:9804600-9807600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr18:9804600-9807800	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr18:9804600-9807800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr18:9804600-9808000	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr18:9804600-9808000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr18:9804600-9808000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
19	chr18:9804600-9808000	Weak transcription	A549	lung
20	chr18:9804600-9808000	Weak transcription	NHDF-Ad	bronchial
21	chr18:9804600-9808000	Weak transcription	Osteobl	bone
22	chr18:9804600-9808200	Weak transcription	Fetal Stomach	stomach
23	chr18:9804600-9808200	Weak transcription	NH-A	brain
24	chr18:9804600-9808600	Weak transcription	Right Atrium	heart
25	chr18:9804600-9808600	Weak transcription	Right Ventricle	heart
26	chr18:9804800-9807400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr18:9804800-9807800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr18:9804800-9807800	Weak transcription	Brain Germinal Matrix	brain
29	chr18:9804800-9807800	Weak transcription	Brain Hippocampus Middle	brain
30	chr18:9804800-9808000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
31	chr18:9804800-9808000	Weak transcription	Aorta	Aorta
32	chr18:9804800-9808000	Weak transcription	Brain Angular Gyrus	brain
33	chr18:9804800-9808000	Weak transcription	Brain Cingulate Gyrus	brain
34	chr18:9804800-9808000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr18:9804800-9808000	Weak transcription	Ovary	ovary
36	chr18:9805000-9807800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr18:9805000-9808000	Weak transcription	Muscle Satellite Cultured Cells	--
38	chr18:9805000-9808000	Weak transcription	Colon Smooth Muscle	Colon
39	chr18:9805000-9808400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr18:9805000-9808400	Weak transcription	Adipose Nuclei	Adipose
41	chr18:9805000-9808400	Weak transcription	Skeletal Muscle Female	skeletal muscle
42	chr18:9805000-9808600	Weak transcription	Brain Anterior Caudate	brain
43	chr18:9805000-9808600	Weak transcription	Esophagus	oesophagus
44	chr18:9805000-9810200	Strong transcription	Primary monocytes fromperipheralblood	blood
45	chr18:9805200-9807400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr18:9805200-9808000	Weak transcription	Stomach Smooth Muscle	stomach
47	chr18:9805200-9808200	Weak transcription	Rectal Smooth Muscle	rectum
48	chr18:9805200-9808400	Weak transcription	Fetal Heart	heart
49	chr18:9805200-9808600	Weak transcription	Left Ventricle	heart
50	chr18:9805400-9811400	Strong transcription	Monocytes-CD14+_RO01746	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links