Variant report

Variant	rs28488039
Chromosome Location	chr1:223251464-223251465
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:223238702..223240898-chr1:223250937..223252895,2	K562	blood:
2	chr1:223248411..223251830-chr1:223252678..223254653,3	K562	blood:
3	chr1:223237955..223240202-chr1:223251395..223253910,2	K562	blood:

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs1624408	1.00[EUR][1000 genomes]
rs1640869	1.00[EUR][1000 genomes]
rs28373518	1.00[EUR][1000 genomes]
rs28445941	1.00[EUR][1000 genomes]
rs28782805	1.00[EUR][1000 genomes]
rs35801972	1.00[EUR][1000 genomes]
rs5744110	1.00[EUR][1000 genomes]
rs6658085	1.00[EUR][1000 genomes]
rs6693240	1.00[EUR][1000 genomes]
rs725972	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999185	chr1:222500725-223278032	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
2	nsv535304	chr1:222500725-223278032	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv1012537	chr1:222755091-223512243	Weak transcription Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
4	nsv1014896	chr1:223070446-223327185	Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv873207	chr1:223078802-223292632	Genic enhancers Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:223246800-223253400	Enhancers	Fetal Muscle Leg	muscle
2	chr1:223247200-223252800	Enhancers	Lung	lung
3	chr1:223247200-223253000	Enhancers	Fetal Lung	lung
4	chr1:223248000-223252600	Enhancers	Fetal Stomach	stomach
5	chr1:223248800-223254400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr1:223249200-223252400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr1:223249200-223252800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr1:223249200-223253000	Enhancers	Left Ventricle	heart
9	chr1:223249200-223253200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr1:223249200-223254600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr1:223249200-223258400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr1:223249400-223252800	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
13	chr1:223249400-223254000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr1:223249800-223252800	Enhancers	Right Atrium	heart
15	chr1:223250600-223252400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr1:223250600-223254400	Weak transcription	Rectal Smooth Muscle	rectum
17	chr1:223250600-223254600	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr1:223250600-223254600	Weak transcription	Fetal Brain Female	brain
19	chr1:223250800-223254600	Weak transcription	Fetal Heart	heart
20	chr1:223251000-223253400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
21	chr1:223251000-223254600	Weak transcription	Esophagus	oesophagus
22	chr1:223251200-223251600	Enhancers	Skeletal Muscle Male	skeletal muscle
23	chr1:223251200-223251800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
24	chr1:223251200-223252000	Enhancers	Skeletal Muscle Female	skeletal muscle
25	chr1:223251200-223252200	Enhancers	Right Ventricle	heart
26	chr1:223251200-223252800	Enhancers	HUES6 Cell Line	embryonic stem cell
27	chr1:223251200-223253000	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr1:223251200-223254400	Weak transcription	HUVEC	blood vessel
29	chr1:223251400-223251600	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr1:223251400-223251600	Enhancers	Stomach Smooth Muscle	stomach
31	chr1:223251400-223254400	Weak transcription	Colon Smooth Muscle	Colon
32	chr1:223251400-223254400	Weak transcription	Fetal Brain Male	brain
33	chr1:223251400-223254600	Enhancers	Placenta	Placenta

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links