Variant report

Variant	rs2176659
Chromosome Location	chr22:27726947-27726948
allele	A/G
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	RAD21	chr22:27726709-27727067	SK-N-SH_RA	brain:	n/a	chr22:27726899-27726909 chr22:27726895-27726914
2	CTCF	chr22:27726880-27727030	HCPEpiC	choroid plexus:	n/a	n/a
3	CTCF	chr22:27726875-27726990	NHEK	skin:	n/a	n/a
4	CTCF	chr22:27726836-27727048	K562	blood:	n/a	n/a
5	CTCF	chr22:27726820-27726970	HRPEpiC	eye:	n/a	n/a
6	CTCF	chr22:27726860-27727010	HMEC	breast:	n/a	n/a
7	CTCF	chr22:27726820-27726970	HRE	kidney:	n/a	n/a
8	CTCF	chr22:27726855-27726990	Pancreas_OC	pancreas:	n/a	n/a
9	RAD21	chr22:27726694-27727019	H1-hESC	embryonic stem cell:	n/a	chr22:27726899-27726909 chr22:27726895-27726914
10	CTCF	chr22:27726882-27726948	MCF-7	breast:	n/a	n/a
11	CTCF	chr22:27726800-27726950	HMF	breast:	n/a	n/a
12	CTCF	chr22:27726840-27726990	BE2_C	brain:	n/a	n/a
13	CTCF	chr22:27726820-27726970	HUVEC	blood vessel:	n/a	n/a
14	CTCF	chr22:27726874-27726960	K562	blood:	n/a	n/a
15	CTCF	chr22:27726900-27727050	HPAF	blood vessel:	n/a	n/a
16	CTCF	chr22:27726897-27726979	A549	lung:	n/a	n/a
17	CTCF	chr22:27726830-27726990	HUVEC	blood vessel:	n/a	n/a
18	RAD21	chr22:27726735-27727048	H1-hESC	embryonic stem cell:	n/a	chr22:27726899-27726909 chr22:27726895-27726914
19	CTCF	chr22:27726840-27726990	HBMEC	blood vessel:	n/a	n/a
20	CTCF	chr22:27726860-27727010	HEK293	kidney:	n/a	n/a
21	RAD21	chr22:27726787-27726997	H1-hESC	embryonic stem cell:	n/a	chr22:27726899-27726909 chr22:27726895-27726914
22	RAD21	chr22:27726550-27727230	SK-N-SH	brain:	n/a	chr22:27727133-27727145 chr22:27726899-27726909 chr22:27726895-27726914
23	E2F4	chr22:27726763-27727007	MCF10A-Er-Src	breast:	n/a	n/a
24	CTCF	chr22:27726800-27726950	HPAF	blood vessel:	n/a	n/a
25	CTCF	chr22:27726800-27726950	WERI-Rb-1	eye:	n/a	n/a
26	RAD21	chr22:27726793-27727011	Hela-S3	cervix:	n/a	chr22:27726899-27726909 chr22:27726895-27726914
27	CTCF	chr22:27726840-27726990	RPTEC	kidney:	n/a	n/a
28	CTCF	chr22:27726885-27726975	MCF-7	breast:	n/a	n/a
29	SMC3	chr22:27726866-27727012	Hela-S3	cervix:	n/a	n/a
30	CTCF	chr22:27726820-27726970	MCF-7	breast:	n/a	n/a
31	CTCF	chr22:27726820-27726970	HEK293	kidney:	n/a	n/a
32	RAD21	chr22:27726736-27726981	SK-N-SH_RA	brain:	n/a	chr22:27726899-27726909 chr22:27726895-27726914

Variant related genes	Relation type
ENSG00000230051	TF binding region

Extended variants
information (count: 9 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs1607498	0.88[MEX][hapmap]
rs16984292	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2139278	0.95[CHB][hapmap];0.84[JPT][hapmap];0.91[ASN][1000 genomes]
rs4822868	0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs567774	0.90[CHB][hapmap];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3413125	chr22:27404463-28121577	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
2	nsv459860	chr22:27527005-28181436	Strong transcription Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv588872	chr22:27527005-28181436	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
4	nsv834166	chr22:27628570-27814359	Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2176659	SLC6A4	trans	lymphoblastoid	seeQTL
rs2176659	C22orf15	cis	cerebellum	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:27715200-27727400	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr22:27722000-27727600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr22:27724600-27729000	Enhancers	Fetal Brain Male	brain
4	chr22:27725800-27727600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr22:27725800-27727600	Weak transcription	Ovary	ovary
6	chr22:27725800-27727800	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr22:27726000-27727600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr22:27726000-27727600	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr22:27726000-27727600	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr22:27726000-27727600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr22:27726200-27727400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr22:27726200-27727600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr22:27726200-27727600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr22:27726200-27727600	Weak transcription	Brain Germinal Matrix	brain
15	chr22:27726400-27727200	Weak transcription	Fetal Brain Female	brain
16	chr22:27726600-27727000	Enhancers	iPS-15b Cell Line	embryonic stem cell
17	chr22:27726600-27727600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links