Variant report

Variant	rs4244628
Chromosome Location	chr1:246945822-246945823
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 62 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10127783	0.91[TSI][hapmap];0.86[EUR][1000 genomes]
rs10159002	0.82[CEU][hapmap];0.86[EUR][1000 genomes]
rs10802442	0.86[EUR][1000 genomes]
rs10924820	0.82[CEU][hapmap];0.89[TSI][hapmap];0.86[EUR][1000 genomes]
rs10924823	0.82[CEU][hapmap];0.91[TSI][hapmap];0.86[EUR][1000 genomes]
rs10924824	0.82[CEU][hapmap];0.91[TSI][hapmap];0.86[EUR][1000 genomes]
rs12049149	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12058428	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12080111	0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12085823	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12090470	0.85[EUR][1000 genomes]
rs12135184	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12144408	0.86[EUR][1000 genomes]
rs34649985	0.86[EUR][1000 genomes]
rs34989088	0.85[EUR][1000 genomes]
rs3795462	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.96[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3795463	0.86[EUR][1000 genomes]
rs3795465	0.92[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3935011	0.85[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4130316	0.85[EUR][1000 genomes]
rs4244627	0.82[CEU][hapmap];0.91[TSI][hapmap];0.86[EUR][1000 genomes]
rs4244630	0.85[EUR][1000 genomes]
rs4926441	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4926448	0.85[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4926451	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4926453	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.96[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4926454	0.86[EUR][1000 genomes]
rs4926455	0.85[EUR][1000 genomes]
rs4926457	0.86[EUR][1000 genomes]
rs60779884	0.82[ASN][1000 genomes]
rs6426328	0.85[CHB][hapmap];0.81[JPT][hapmap];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6426331	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6426332	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6426334	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6664091	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6664883	0.82[CEU][hapmap];0.86[EUR][1000 genomes]
rs6686584	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7513803	1.00[CEU][hapmap];0.87[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7537149	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7549965	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7556120	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9426267	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:20 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949571	chr1:246688635-247240863	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	nsv873421	chr1:246818634-247044692	Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	esv2762192	chr1:246823857-247069232	Weak transcription Strong transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	nsv1006271	chr1:246832606-247276182	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
5	nsv535416	chr1:246832606-247276182	Strong transcription ZNF genes & repeats Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
6	nsv430413	chr1:246845971-246975015	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
7	nsv873422	chr1:246854862-247002638	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
8	nsv1011346	chr1:246868799-247133898	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
9	nsv1006262	chr1:246892826-246964775	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
10	nsv523531	chr1:246893948-246967899	Enhancers Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
11	nsv999756	chr1:246894542-246969660	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer 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	14 gene(s)	inside rSNPs	diseases
12	nsv1009436	chr1:246910373-246965832	Bivalent/Poised TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
13	nsv873423	chr1:246923861-246978504	Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Weak transcription Active TSS Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
14	nsv549545	chr1:246936353-246963019	Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
15	esv2756894	chr1:246939856-246946021	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
16	esv2759013	chr1:246939856-246946021	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
17	esv3408268	chr1:246944429-246948627	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
18	esv1841827	chr1:246944502-246954313	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
19	esv3491345	chr1:246945629-246947627	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
20	esv3491346	chr1:246945629-246947627	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4244628	SCCPDH	cis	lymphoblastoid	seeQTL

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:246888400-246946400	Weak transcription	Small Intestine	intestine
2	chr1:246902800-246952800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:246925200-246952200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr1:246932400-246952000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr1:246932600-246948000	Strong transcription	Liver	Liver
6	chr1:246932600-246948600	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr1:246932600-246948600	Weak transcription	Esophagus	oesophagus
8	chr1:246932800-246948800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr1:246932800-246952400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr1:246932800-246956400	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr1:246938400-246947200	Strong transcription	Fetal Intestine Small	intestine
12	chr1:246940200-246947600	Weak transcription	HUVEC	blood vessel
13	chr1:246940200-246948800	Weak transcription	Fetal Brain Male	brain
14	chr1:246940400-246949000	Weak transcription	Rectal Smooth Muscle	rectum
15	chr1:246940600-246948600	Weak transcription	Brain Angular Gyrus	brain
16	chr1:246940600-246948800	Weak transcription	Brain Cingulate Gyrus	brain
17	chr1:246940600-246948800	Weak transcription	Fetal Kidney	kidney
18	chr1:246940800-246948000	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr1:246940800-246951600	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr1:246940800-246951600	Weak transcription	HUES64 Cell Line	embryonic stem cell
21	chr1:246941200-246948200	Weak transcription	Duodenum Mucosa	Duodenum
22	chr1:246941200-246952600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr1:246941600-246948800	Weak transcription	Colonic Mucosa	Colon
24	chr1:246941600-246948800	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr1:246941600-246952200	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr1:246942200-246949000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr1:246942800-246952200	Weak transcription	Fetal Brain Female	brain
28	chr1:246943000-246948000	Enhancers	Primary hematopoietic stem cells	blood
29	chr1:246943400-246952000	Weak transcription	Brain Anterior Caudate	brain
30	chr1:246944200-246947800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr1:246944400-246948800	Weak transcription	Gastric	stomach
32	chr1:246944600-246946200	Enhancers	K562	blood
33	chr1:246944600-246946400	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr1:246944600-246947800	Genic enhancers	Fetal Muscle Trunk	muscle
35	chr1:246944600-246952200	Weak transcription	NH-A	brain
36	chr1:246944800-246946000	Enhancers	NHDF-Ad	bronchial
37	chr1:246944800-246946200	Enhancers	Primary monocytes fromperipheralblood	blood
38	chr1:246944800-246946200	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
39	chr1:246944800-246946800	Weak transcription	Fetal Lung	lung
40	chr1:246944800-246947800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr1:246944800-246948200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr1:246944800-246952000	Weak transcription	Fetal Intestine Large	intestine
43	chr1:246944800-246952200	Weak transcription	Placenta Amnion	Placenta Amnion
44	chr1:246945000-246946000	Weak transcription	Lung	lung
45	chr1:246945000-246946000	Enhancers	Dnd41	blood
46	chr1:246945000-246946200	Enhancers	HepG2	liver
47	chr1:246945000-246946400	Enhancers	HSMMtube	muscle
48	chr1:246945000-246946800	Weak transcription	Placenta	Placenta
49	chr1:246945000-246947000	Enhancers	HSMM	muscle
50	chr1:246945000-246948800	Weak transcription	Brain Germinal Matrix	brain

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