Variant report

Variant	rs2241943
Chromosome Location	chr18:9522666-9522667
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	KAP1	chr18:9522266-9522862	U2OS	brain:	n/a	n/a
2	FOXA2	chr18:9522564-9522835	HepG2	liver:	n/a	n/a
3	ZNF263	chr18:9521958-9524049	HEK293-T-REx	kidney:	n/a	chr18:9522777-9522786
4	TCF7L2	chr18:9522341-9523305	HEK293	kidney:	n/a	chr18:9523206-9523215 chr18:9522727-9522736
5	TCF7L2	chr18:9522552-9522935	HepG2	liver:	n/a	chr18:9522727-9522736

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr18:9516467..9518987-chr18:9520554..9522788,2	MCF-7	breast:
2	chr18:9518087..9520261-chr18:9521010..9523550,2	K562	blood:

Variant related genes	Relation type
RNU2-27P	TF binding region
ENSG00000273352	Chromatin interaction
ENSG00000251994	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10468796	0.94[ASN][1000 genomes]
rs10468797	0.91[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs10853380	1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs10898	0.91[CHB][hapmap]
rs11663979	0.95[ASN][1000 genomes]
rs12386073	0.89[ASN][1000 genomes]
rs12386075	0.95[ASN][1000 genomes]
rs12386078	0.93[ASN][1000 genomes]
rs12454651	0.94[ASN][1000 genomes]
rs12454987	0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs12457895	0.92[ASN][1000 genomes]
rs1561997	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1561998	0.87[CHB][hapmap]
rs16955157	0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2028660	0.95[ASN][1000 genomes]
rs2061692	0.86[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs28510500	0.95[ASN][1000 genomes]
rs329006	0.87[CHB][hapmap]
rs329007	0.87[CHB][hapmap]
rs4798819	0.95[ASN][1000 genomes]
rs58103465	0.88[ASN][1000 genomes]
rs58651706	0.86[ASN][1000 genomes]
rs59277394	0.95[ASN][1000 genomes]
rs62086154	0.91[ASN][1000 genomes]
rs62087367	0.95[ASN][1000 genomes]
rs62087375	0.94[ASN][1000 genomes]
rs7234529	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7235585	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7238922	0.98[ASN][1000 genomes]
rs73395727	0.94[ASN][1000 genomes]
rs8092935	0.87[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916373	chr18:9026803-9592201	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
2	nsv1056407	chr18:9144345-9553764	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
3	nsv1062025	chr18:9287249-9552470	Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
4	nsv543643	chr18:9287249-9552470	ZNF genes & repeats Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
5	nsv833585	chr18:9401630-9597291	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
6	nsv428005	chr18:9401658-9542396	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
7	esv3693417	chr18:9512985-9693638	Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2241943	SLMO1	cis	parietal	SCAN
rs2241943	RALBP1	cis	multi-tissue	Pritchard
rs2241943	PTPRM	cis	parietal	SCAN
rs2241943	RALBP1	cis	Whole Blood	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:9479000-9533200	Weak transcription	Aorta	Aorta
2	chr18:9479000-9533600	Weak transcription	Gastric	stomach
3	chr18:9495200-9530400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
4	chr18:9495200-9533600	Weak transcription	Right Ventricle	heart
5	chr18:9495400-9524000	Weak transcription	Spleen	Spleen
6	chr18:9495400-9534000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr18:9496800-9534000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr18:9497400-9532600	Weak transcription	Colonic Mucosa	Colon
9	chr18:9498400-9523200	Weak transcription	Esophagus	oesophagus
10	chr18:9499400-9525000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr18:9500800-9535000	Weak transcription	Fetal Heart	heart
12	chr18:9505200-9524600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr18:9506800-9532000	Weak transcription	Pancreas	Pancrea
14	chr18:9508000-9531600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr18:9508600-9525200	Weak transcription	Brain Germinal Matrix	brain
16	chr18:9508600-9531800	Weak transcription	Small Intestine	intestine
17	chr18:9512200-9524600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr18:9512800-9524400	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr18:9513200-9524600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr18:9513200-9526600	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr18:9513200-9534000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr18:9513600-9537800	Weak transcription	Fetal Brain Male	brain
23	chr18:9514200-9523200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr18:9514400-9524000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr18:9514600-9524600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr18:9514600-9528800	Weak transcription	NH-A	brain
27	chr18:9514600-9530200	Weak transcription	Rectal Smooth Muscle	rectum
28	chr18:9515600-9526800	Weak transcription	A549	lung
29	chr18:9516200-9526800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr18:9517400-9523600	Weak transcription	Osteobl	bone
31	chr18:9517600-9524400	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr18:9517600-9526400	Weak transcription	Brain Anterior Caudate	brain
33	chr18:9517800-9534000	Weak transcription	NHLF	lung
34	chr18:9518200-9528400	Weak transcription	HUVEC	blood vessel
35	chr18:9518200-9533600	Weak transcription	Brain Substantia Nigra	brain
36	chr18:9518400-9526400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
37	chr18:9518400-9526400	Weak transcription	NHEK	skin
38	chr18:9518400-9526800	Weak transcription	H9 Cell Line	embryonic stem cell
39	chr18:9518600-9523200	Weak transcription	Cortex derived primary cultured neurospheres	brain
40	chr18:9518600-9524800	Weak transcription	GM12878-XiMat	blood
41	chr18:9518800-9534400	Weak transcription	Pancreatic Islets	Pancreatic Islet
42	chr18:9520000-9532000	Weak transcription	Colon Smooth Muscle	Colon
43	chr18:9520400-9524600	Weak transcription	Brain Angular Gyrus	brain
44	chr18:9520400-9534800	Weak transcription	Psoas Muscle	Psoas
45	chr18:9521000-9522800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr18:9521200-9523400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr18:9521200-9526800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr18:9521400-9527400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
49	chr18:9521400-9535000	Strong transcription	Fetal Muscle Leg	muscle
50	chr18:9521400-9541800	Strong transcription	Fetal Stomach	stomach

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