Variant report

Variant	rs16865625
Chromosome Location	chr2:178557852-178557853
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:178557827..178560384-chr2:178566181..178567818,2	K562	blood:
2	chr2:178553724..178556122-chr2:178557669..178561053,4	K562	blood:
3	chr2:178536377..178538004-chr2:178556463..178558808,2	K562	blood:
4	chr2:178556581..178559111-chr2:178571009..178573713,2	K562	blood:
5	chr2:178557613..178559704-chr2:178561778..178563487,2	K562	blood:

Variant related genes	Relation type
ENSG00000229941	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10497487	0.90[YRI][hapmap]
rs10497490	0.91[YRI][hapmap];0.87[AFR][1000 genomes]
rs10497491	0.92[YRI][hapmap];0.87[AFR][1000 genomes]
rs1561316	0.92[YRI][hapmap];0.82[AFR][1000 genomes]
rs1561317	0.87[YRI][hapmap];0.87[AFR][1000 genomes]
rs16865617	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16865641	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16865642	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16865643	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16865645	0.85[YRI][hapmap]
rs16865647	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16865651	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16865668	0.91[YRI][hapmap];0.87[AFR][1000 genomes]
rs16865670	0.87[AFR][1000 genomes]
rs16865676	0.91[YRI][hapmap];0.87[AFR][1000 genomes]
rs16865678	0.84[YRI][hapmap]
rs16865684	0.91[YRI][hapmap];0.87[AFR][1000 genomes]
rs16865689	0.92[YRI][hapmap];0.82[AFR][1000 genomes]
rs16865694	0.92[YRI][hapmap];0.87[AFR][1000 genomes]
rs16865697	0.92[YRI][hapmap];0.87[AFR][1000 genomes]
rs16865703	0.91[YRI][hapmap];0.87[AFR][1000 genomes]
rs16865711	0.91[YRI][hapmap];0.87[AFR][1000 genomes]
rs16865776	0.83[YRI][hapmap]
rs4464320	0.87[AFR][1000 genomes]
rs4541282	0.92[YRI][hapmap];0.87[AFR][1000 genomes]
rs4585066	0.86[YRI][hapmap];0.87[AFR][1000 genomes]
rs73028304	1.00[AMR][1000 genomes]
rs934808	0.91[YRI][hapmap];0.87[AFR][1000 genomes]
rs934810	0.87[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999086	chr2:178262348-178773585	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv536055	chr2:178262348-178773585	Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	nsv431812	chr2:178525371-178584470	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1007925	chr2:178535922-178577002	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv870023	chr2:178545623-178581407	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv1005854	chr2:178546907-178586608	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	esv2762967	chr2:178546919-178577002	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv1005991	chr2:178550049-178577002	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	nsv528219	chr2:178551924-178567151	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv1003983	chr2:178551958-178577002	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:178555000-178558600	Weak transcription	Stomach Mucosa	stomach
2	chr2:178555400-178559200	Enhancers	Pancreatic Islets	Pancreatic Islet
3	chr2:178555400-178559800	Enhancers	Fetal Kidney	kidney
4	chr2:178556200-178558000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr2:178556400-178558400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr2:178556400-178558400	Enhancers	Hela-S3	cervix
7	chr2:178556400-178558600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr2:178556600-178558000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr2:178556600-178558200	Enhancers	NHEK	skin
10	chr2:178556800-178558000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr2:178557000-178558000	Enhancers	Fetal Intestine Large	intestine
12	chr2:178557000-178558200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr2:178557000-178558200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr2:178557000-178558200	Enhancers	HMEC	breast
15	chr2:178557000-178558400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr2:178557200-178558000	Enhancers	Duodenum Mucosa	Duodenum
17	chr2:178557200-178558200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr2:178557200-178558200	Enhancers	Fetal Intestine Small	intestine
19	chr2:178557400-178560200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr2:178557600-178558000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr2:178557600-178558000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
22	chr2:178557600-178558200	Enhancers	Pancreas	Pancrea
23	chr2:178557600-178559200	Enhancers	Liver	Liver
24	chr2:178557800-178558200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr2:178557800-178558200	Enhancers	Gastric	stomach
26	chr2:178557800-178558200	Enhancers	A549	lung
27	chr2:178557800-178558400	Enhancers	Ovary	ovary
28	chr2:178557800-178558400	Enhancers	HepG2	liver
29	chr2:178557800-178559200	Enhancers	K562	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links