Variant report

Variant	rs1198842
Chromosome Location	chr2:10905196-10905197
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:10875606..10877816-chr2:10902638..10905223,2	MCF-7	breast:
2	chr2:10905117..10907508-chr2:10909439..10912391,2	K562	blood:
3	chr2:10897911..10900939-chr2:10902372..10905567,4	MCF-7	breast:
4	chr2:10897105..10899038-chr2:10904110..10905856,2	MCF-7	breast:
5	chr2:10902594..10905238-chr2:10911928..10914865,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000272275	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs11678994	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1198843	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1198848	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1198849	0.88[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12611921	0.92[ASN][1000 genomes]
rs1387572	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1734413	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2171773	0.86[ASN][1000 genomes]
rs57127376	0.89[ASN][1000 genomes]
rs6757005	0.85[ASN][1000 genomes]
rs902130	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][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	nsv1000953	chr2:10717304-10921805	Strong transcription Enhancers Active TSS Bivalent Enhancer Genic enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	nsv535584	chr2:10717304-10921805	Bivalent Enhancer Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	nsv833381	chr2:10723465-10911284	Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv1000731	chr2:10758657-10943882	Strong transcription Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
5	esv3427047	chr2:10900130-10906802	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Genic enhancers	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:10892600-10905400	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr2:10897800-10906400	Enhancers	Placenta	Placenta
3	chr2:10899800-10905200	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr2:10899800-10908200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr2:10900000-10905400	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr2:10902200-10905400	Weak transcription	Esophagus	oesophagus
7	chr2:10903400-10908200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr2:10903400-10908200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr2:10903400-10914400	Weak transcription	Right Atrium	heart
10	chr2:10903600-10905200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr2:10903600-10908200	Weak transcription	Right Ventricle	heart
12	chr2:10903600-10914400	Weak transcription	Gastric	stomach
13	chr2:10903800-10905200	Weak transcription	Fetal Intestine Small	intestine
14	chr2:10903800-10905600	Weak transcription	Lung	lung
15	chr2:10904200-10905400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr2:10904200-10916400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr2:10904400-10908200	Weak transcription	Fetal Muscle Leg	muscle
18	chr2:10904600-10905800	Weak transcription	Spleen	Spleen
19	chr2:10904600-10916400	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr2:10904800-10915200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr2:10905000-10905400	Enhancers	Hela-S3	cervix
22	chr2:10905000-10906400	Enhancers	Fetal Intestine Large	intestine

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links