Variant report

Variant	rs2103641
Chromosome Location	chr1:169864998-169864999
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	NFYB	chr1:169864848-169865187	GM12878	blood:	n/a	n/a
2	JUN	chr1:169861838-169865596	K562	blood:	n/a	chr1:169863455-169863464 chr1:169863451-169863464 chr1:169863477-169863486
3	BATF	chr1:169864809-169865538	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:169863583..169866323-chr1:169872602..169875354,3	MCF-7	breast:
2	chr1:169862596..169865250-chr1:170499667..170504019,5	K562	blood:
3	chr1:169862177..169865166-chr1:170500254..170502788,2	MCF-7	breast:
4	chr1:169863487..169865405-chr1:169882715..169884373,2	K562	blood:
5	chr1:169763994..169765974-chr1:169862962..169865288,2	K562	blood:

Variant related genes	Relation type
SCYL3	TF binding region
ENSG00000000460	Chromatin interaction
ENSG00000231407	Chromatin interaction
ENSG00000120370	Chromatin interaction
ENSG00000171806	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10458398	1.00[ASN][1000 genomes]
rs10800487	1.00[ASN][1000 genomes]
rs10919267	0.84[ASN][1000 genomes]
rs10919268	1.00[ASN][1000 genomes]
rs10919269	1.00[ASN][1000 genomes]
rs10919276	1.00[EUR][1000 genomes]
rs10919288	1.00[EUR][1000 genomes]
rs10919294	1.00[EUR][1000 genomes]
rs10919295	1.00[EUR][1000 genomes]
rs10919296	1.00[EUR][1000 genomes]
rs10919300	1.00[EUR][1000 genomes]
rs12023729	1.00[ASN][1000 genomes]
rs12024570	1.00[ASN][1000 genomes]
rs12025296	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12027790	1.00[ASN][1000 genomes]
rs12035711	1.00[ASN][1000 genomes]
rs12044536	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12066551	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12071325	1.00[EUR][1000 genomes]
rs12076018	1.00[EUR][1000 genomes]
rs12077708	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12079608	1.00[EUR][1000 genomes]
rs12083317	1.00[ASN][1000 genomes]
rs12090220	1.00[EUR][1000 genomes]
rs12095784	1.00[EUR][1000 genomes]
rs13374781	1.00[EUR][1000 genomes]
rs13375701	1.00[EUR][1000 genomes]
rs16862886	1.00[EUR][1000 genomes]
rs16862978	1.00[EUR][1000 genomes]
rs2272912	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2272915	1.00[ASN][1000 genomes]
rs2901261	1.00[EUR][1000 genomes]
rs4279900	1.00[EUR][1000 genomes]
rs56084868	1.00[EUR][1000 genomes]
rs57038529	1.00[EUR][1000 genomes]
rs73041439	1.00[EUR][1000 genomes]
rs74121797	1.00[EUR][1000 genomes]
rs74122312	1.00[EUR][1000 genomes]
rs74122421	1.00[EUR][1000 genomes]
rs74122422	1.00[EUR][1000 genomes]
rs74122452	1.00[EUR][1000 genomes]
rs7531947	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7532990	1.00[ASN][1000 genomes]
rs7533350	1.00[ASN][1000 genomes]
rs989054	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3451367	chr1:169630075-169976964	Strong transcription Flanking Active TSS Genic enhancers Enhancers Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	esv1814601	chr1:169782006-169885186	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	esv1821503	chr1:169782006-169885186	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	esv1847722	chr1:169782006-169885186	Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
5	esv2757760	chr1:169782006-169885186	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
6	esv2758976	chr1:169782006-169885186	Strong transcription Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
7	nsv428268	chr1:169782006-169885186	Strong transcription ZNF genes & repeats Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
8	esv1845220	chr1:169782006-169933886	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169863400-169865400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr1:169863800-169868400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr1:169864000-169865400	Enhancers	H1 Cell Line	embryonic stem cell
4	chr1:169864000-169865400	Enhancers	HUES48 Cell Line	embryonic stem cell
5	chr1:169864000-169865400	Enhancers	Primary monocytes fromperipheralblood	blood
6	chr1:169864000-169865600	Enhancers	GM12878-XiMat	blood
7	chr1:169864000-169868800	Weak transcription	Fetal Intestine Small	intestine
8	chr1:169864000-169869000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr1:169864000-169869000	Weak transcription	HMEC	breast
10	chr1:169864200-169865000	Weak transcription	Primary neutrophils fromperipheralblood	blood
11	chr1:169864200-169865400	Enhancers	iPS-18 Cell Line	embryonic stem cell
12	chr1:169864200-169866400	Enhancers	K562	blood
13	chr1:169864200-169867200	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr1:169864200-169868400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr1:169864200-169869000	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr1:169864400-169868200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr1:169864600-169865000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr1:169864600-169865600	Enhancers	Monocytes-CD14+_RO01746	blood
19	chr1:169864800-169865400	Enhancers	Primary hematopoietic stem cells short term culture	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links