Variant report

Variant	rs10916244
Chromosome Location	chr1:228108703-228108704
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:228104214..228105732-chr1:228108237..228110826,2	MCF-7	breast:
2	chr1:227652761..227655179-chr1:228106807..228109006,2	MCF-7	breast:
3	chr1:228102507..228105005-chr1:228106646..228109537,2	MCF-7	breast:
4	chr1:227912717..227914505-chr1:228107009..228109578,2	K562	blood:

Extended variants
information (count: 20 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs10127943	0.86[CHB][hapmap];0.81[CHD][hapmap]
rs12741282	0.97[EUR][1000 genomes]
rs12748472	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2796055	0.80[CEU][hapmap]
rs587000	0.80[CEU][hapmap]
rs680148	0.80[CEU][hapmap]
rs849900	0.80[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010605	chr1:227770415-228332690	Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
2	esv32853	chr1:227880116-228806209	Enhancers Genic enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	187 gene(s)	inside rSNPs	diseases
3	nsv427952	chr1:227881664-228308629	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
4	nsv826908	chr1:227895386-228691100	Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
5	nsv873249	chr1:227920061-228121548	Weak transcription Bivalent Enhancer Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
6	nsv1005852	chr1:227957099-228148363	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
7	nsv535319	chr1:227957099-228148363	Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
8	nsv516409	chr1:228035131-228296745	Enhancers Genic enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
9	nsv523935	chr1:228038124-228681749	Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	137 gene(s)	inside rSNPs	diseases
10	nsv873250	chr1:228051234-228121548	Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
11	nsv873251	chr1:228051234-228160911	Enhancers Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Weak 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 miRNA	6 gene(s)	inside rSNPs	diseases
12	nsv826920	chr1:228106910-228116488	Genic enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
13	esv3391638	chr1:228108379-228111177	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10916244	GUK1	cis	parietal	SCAN
rs10916244	NUP133	cis	parietal	SCAN
rs10916244	SNAP47	cis	cerebellum	SCAN
rs10916244	ACBD3	cis	cerebellum	SCAN

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:228075600-228109200	Weak transcription	Right Atrium	heart
2	chr1:228098600-228117600	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr1:228098800-228122800	Weak transcription	HSMMtube	muscle
4	chr1:228099400-228108800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr1:228099400-228122400	Weak transcription	HSMM	muscle
6	chr1:228101200-228110400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr1:228101400-228111000	Weak transcription	Fetal Brain Female	brain
8	chr1:228103800-228113800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr1:228103800-228117000	Weak transcription	Fetal Intestine Large	intestine
10	chr1:228104200-228111000	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr1:228104600-228110400	Weak transcription	Fetal Lung	lung
12	chr1:228105200-228108800	Weak transcription	HMEC	breast
13	chr1:228105200-228112400	Weak transcription	Brain Germinal Matrix	brain
14	chr1:228105200-228112800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr1:228105600-228110200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr1:228106600-228121400	Weak transcription	Psoas Muscle	Psoas
17	chr1:228106800-228109000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr1:228106800-228110200	Strong transcription	Stomach Smooth Muscle	stomach
19	chr1:228107200-228109000	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr1:228107200-228109000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr1:228107400-228109200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr1:228107400-228109200	Strong transcription	Pancreas	Pancrea
23	chr1:228107600-228109600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
24	chr1:228107600-228110000	Weak transcription	Brain Angular Gyrus	brain
25	chr1:228107600-228112200	Weak transcription	Fetal Heart	heart
26	chr1:228107800-228109000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr1:228107800-228110000	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr1:228107800-228111400	Weak transcription	Rectal Smooth Muscle	rectum
29	chr1:228107800-228134400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr1:228108000-228109600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr1:228108000-228110000	Strong transcription	Fetal Stomach	stomach
32	chr1:228108000-228110200	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr1:228108000-228110600	Weak transcription	HUES6 Cell Line	embryonic stem cell
34	chr1:228108200-228113000	Weak transcription	Colonic Mucosa	Colon
35	chr1:228108200-228113600	Strong transcription	Placenta Amnion	Placenta Amnion
36	chr1:228108400-228108800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
37	chr1:228108400-228109400	Strong transcription	Colon Smooth Muscle	Colon
38	chr1:228108400-228109600	Strong transcription	Gastric	stomach
39	chr1:228108400-228109800	Strong transcription	Ovary	ovary
40	chr1:228108400-228109800	Strong transcription	Right Ventricle	heart
41	chr1:228108400-228109800	Strong transcription	Spleen	Spleen
42	chr1:228108400-228111000	Strong transcription	Skeletal Muscle Male	skeletal muscle
43	chr1:228108400-228112400	Strong transcription	Skeletal Muscle Female	skeletal muscle
44	chr1:228108600-228108800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr1:228108600-228109200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
46	chr1:228108600-228109200	Strong transcription	Duodenum Smooth Muscle	Duodenum
47	chr1:228108600-228109200	ZNF genes & repeats	Esophagus	oesophagus
48	chr1:228108600-228109800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr1:228108600-228109800	Strong transcription	Lung	lung
50	chr1:228108600-228110000	Strong transcription	Fetal Intestine Small	intestine

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links