Variant report

Variant	rs1063178
Chromosome Location	chr1:161721707-161721708
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:161719443..161721129-chr1:161721357..161723660,2	MCF-7	breast:
2	chr1:161718595..161726705-chr1:161728119..161739561,22	MCF-7	breast:
3	chr1:161703503..161707776-chr1:161717836..161724077,7	K562	blood:
4	chr1:161718568..161724937-chr1:161732191..161738837,13	K562	blood:
5	chr1:161718558..161723568-chr1:161731521..161737462,16	K562	blood:
6	chr1:161719690..161721736-chr1:161980982..161982945,2	MCF-7	breast:
7	chr1:161704696..161707209-chr1:161718366..161721899,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000241347	Chromatin interaction
ENSG00000118217	Chromatin interaction
ENSG00000226889	Chromatin interaction
ENSG00000081721	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs1027702	0.93[GIH][hapmap];0.84[TSI][hapmap]
rs10917821	1.00[CEU][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12121310	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12121500	0.82[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12121522	0.93[GIH][hapmap];0.84[TSI][hapmap]
rs12745240	1.00[ASW][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.91[MEX][hapmap];0.97[MKK][hapmap];0.84[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs1340981	0.93[GIH][hapmap];0.84[TSI][hapmap]
rs1417580	0.82[GIH][hapmap]
rs16852851	0.89[YRI][hapmap]
rs2066247	0.82[GIH][hapmap]
rs2174209	0.97[ASN][1000 genomes]
rs34963459	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35541527	0.89[YRI][hapmap]
rs4532807	0.85[YRI][hapmap]
rs4656332	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4657096	0.93[GIH][hapmap];0.84[TSI][hapmap]
rs6427625	0.81[EUR][1000 genomes]
rs6427626	0.82[GIH][hapmap]
rs71634909	0.86[AFR][1000 genomes]
rs953301	0.81[YRI][hapmap]

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	nsv428257	chr1:161406315-161868263	Bivalent/Poised TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	esv33393	chr1:161478681-162080327	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
3	nsv464184	chr1:161646807-161885352	Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
4	nsv548075	chr1:161646807-161885352	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking 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	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1063178	C1orf61	cis	cerebellum	SCAN
rs1063178	FCRL1	cis	cerebellum	SCAN
rs1063178	ARHGEF11	cis	cerebellum	SCAN
rs1063178	PEAR1	cis	parietal	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:161720400-161734600	Weak transcription	Aorta	Aorta
2	chr1:161720600-161722000	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr1:161720600-161722400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr1:161720600-161724200	Weak transcription	Esophagus	oesophagus
5	chr1:161720600-161728800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr1:161720600-161734600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr1:161720600-161734800	Weak transcription	Psoas Muscle	Psoas
8	chr1:161720600-161736000	Weak transcription	Spleen	Spleen
9	chr1:161720800-161721800	Weak transcription	Colon Smooth Muscle	Colon
10	chr1:161720800-161722400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr1:161720800-161734600	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr1:161720800-161735000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr1:161720800-161735000	Weak transcription	Stomach Mucosa	stomach
14	chr1:161721000-161721800	Weak transcription	Brain Angular Gyrus	brain
15	chr1:161721000-161722000	Enhancers	Fetal Brain Male	brain
16	chr1:161721000-161723600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr1:161721000-161726800	Strong transcription	Fetal Lung	lung
18	chr1:161721000-161728200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
19	chr1:161721000-161728800	Strong transcription	HUES48 Cell Line	embryonic stem cell
20	chr1:161721000-161728800	Strong transcription	HUES6 Cell Line	embryonic stem cell
21	chr1:161721000-161728800	Strong transcription	HUES64 Cell Line	embryonic stem cell
22	chr1:161721000-161728800	Strong transcription	Placenta	Placenta
23	chr1:161721000-161734600	Weak transcription	Right Ventricle	heart
24	chr1:161721000-161734600	Weak transcription	HSMMtube	muscle
25	chr1:161721000-161735000	Weak transcription	Fetal Heart	heart
26	chr1:161721200-161721800	Genic enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr1:161721200-161721800	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr1:161721200-161721800	Genic enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr1:161721200-161721800	Weak transcription	Left Ventricle	heart
30	chr1:161721200-161721800	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr1:161721200-161721800	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr1:161721200-161722000	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr1:161721200-161722000	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr1:161721200-161722000	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
35	chr1:161721200-161722200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr1:161721200-161722200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr1:161721200-161722400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr1:161721200-161722400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
39	chr1:161721200-161722400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
40	chr1:161721200-161722400	Weak transcription	Fetal Intestine Small	intestine
41	chr1:161721200-161722400	Weak transcription	Gastric	stomach
42	chr1:161721200-161722400	Weak transcription	Lung	lung
43	chr1:161721200-161722400	Weak transcription	Small Intestine	intestine
44	chr1:161721200-161722800	Weak transcription	Colonic Mucosa	Colon
45	chr1:161721200-161722800	Weak transcription	Ovary	ovary
46	chr1:161721200-161722800	Weak transcription	Rectal Smooth Muscle	rectum
47	chr1:161721200-161723000	Genic enhancers	Dnd41	blood
48	chr1:161721200-161723400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
49	chr1:161721200-161723400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
50	chr1:161721200-161723400	Weak transcription	Brain Substantia Nigra	brain

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