Variant report

Variant	rs6434220
Chromosome Location	chr2:188401993-188401994
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:188367231..188371096-chr2:188401019..188405423,6	K562	blood:
2	chr2:188395123..188398204-chr2:188399307..188403080,4	K562	blood:

Extended variants
information (count: 31 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs12998073	0.81[AFR][1000 genomes]
rs13035938	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.94[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16829088	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34893125	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35612915	0.86[EUR][1000 genomes]
rs35721125	0.81[EUR][1000 genomes]
rs35935664	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7573488	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8176479	0.81[CEU][hapmap];0.81[GIH][hapmap];0.88[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:22 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv875560	chr2:188219052-188508011	Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv875561	chr2:188226900-188440752	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
3	nsv875564	chr2:188258904-188414161	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
4	nsv875565	chr2:188258904-188440752	Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
5	nsv875566	chr2:188258904-188626214	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
6	nsv875567	chr2:188258904-188673462	Flanking Active TSS ZNF genes & repeats Active TSS Weak transcription Enhancers Strong transcription 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	8 gene(s)	inside rSNPs	diseases
7	nsv834488	chr2:188268434-188415496	Enhancers Strong transcription Active TSS Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
8	nsv875568	chr2:188291105-188653806	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Strong transcription 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	7 gene(s)	inside rSNPs	diseases
9	nsv875576	chr2:188343497-188482933	Transcr. at gene 5' and 3' Genic enhancers Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv875577	chr2:188343497-188500930	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
11	nsv875578	chr2:188343497-188690187	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
12	nsv997899	chr2:188356689-188531831	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
13	nsv1014298	chr2:188359747-188531831	Genic enhancers Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
14	nsv1013166	chr2:188359747-188544803	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
15	nsv1014942	chr2:188360116-188480738	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
16	nsv584038	chr2:188370232-188450136	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
17	nsv875580	chr2:188370232-188521234	Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
18	esv2757845	chr2:188380042-188503185	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
19	esv2759108	chr2:188380042-188503185	ZNF genes & repeats Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
20	nsv875581	chr2:188390819-188521234	Enhancers Strong transcription Weak transcription Bivalent Enhancer Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
21	nsv875582	chr2:188395700-188508011	Enhancers Flanking Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
22	nsv875583	chr2:188395700-188521234	Active TSS Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs6434220	ASNSD1	cis	cerebellum	SCAN
rs6434220	ORMDL1	cis	cerebellum	SCAN
rs6434220	C2orf88	cis	parietal	SCAN
rs6434220	CALCRL	cis	cerebellum	SCAN
rs6434220	CALCRL	cis	multi-tissue	Pritchard

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:188381800-188406000	Weak transcription	Small Intestine	intestine
2	chr2:188381800-188406600	Weak transcription	Aorta	Aorta
3	chr2:188385200-188406000	Weak transcription	Skeletal Muscle Female	skeletal muscle
4	chr2:188387000-188406000	Weak transcription	Fetal Intestine Large	intestine
5	chr2:188387200-188406000	Weak transcription	HSMMtube	muscle
6	chr2:188391800-188405800	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr2:188392200-188402000	Weak transcription	Fetal Lung	lung
8	chr2:188392200-188413200	Weak transcription	Psoas Muscle	Psoas
9	chr2:188392400-188409200	Weak transcription	Ovary	ovary
10	chr2:188393000-188404800	Weak transcription	NH-A	brain
11	chr2:188393000-188406200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr2:188394800-188405800	Weak transcription	NHLF	lung
13	chr2:188394800-188408400	Weak transcription	K562	blood
14	chr2:188395400-188402800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr2:188395400-188405800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr2:188395600-188404200	Weak transcription	NHDF-Ad	bronchial
17	chr2:188396000-188404800	Weak transcription	Osteobl	bone
18	chr2:188397400-188403800	Weak transcription	Hela-S3	cervix
19	chr2:188397600-188403800	Weak transcription	A549	lung
20	chr2:188397800-188405800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr2:188397800-188406400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr2:188398000-188402800	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr2:188398000-188403200	Weak transcription	HSMM	muscle
24	chr2:188398000-188409200	Weak transcription	Fetal Muscle Trunk	muscle
25	chr2:188398200-188404800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr2:188398200-188404800	Weak transcription	Fetal Stomach	stomach
27	chr2:188398200-188406000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr2:188398200-188406000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr2:188398200-188406000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr2:188398200-188406000	Weak transcription	Fetal Intestine Small	intestine
31	chr2:188398200-188409200	Weak transcription	Lung	lung
32	chr2:188398200-188409200	Weak transcription	Pancreas	Pancrea
33	chr2:188398200-188409600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr2:188398200-188409600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
35	chr2:188398400-188403600	Weak transcription	HUVEC	blood vessel
36	chr2:188398400-188403800	Weak transcription	HepG2	liver
37	chr2:188398400-188404600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr2:188398400-188406600	Weak transcription	Placenta	Placenta
39	chr2:188398400-188418000	Weak transcription	Placenta Amnion	Placenta Amnion
40	chr2:188398600-188403600	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr2:188400000-188405800	Weak transcription	Liver	Liver
42	chr2:188400600-188404000	Weak transcription	HUES48 Cell Line	embryonic stem cell
43	chr2:188401800-188408000	Weak transcription	Primary hematopoietic stem cells	blood

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