Variant report

Variant	rs4656724
Chromosome Location	chr1:169821488-169821489
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:169821063..169825136-chr1:169860928..169863692,3	K562	blood:
2	chr1:169762571..169765359-chr1:169821274..169823423,2	K562	blood:
3	chr1:169820262..169822965-chr1:169860933..169863920,2	MCF-7	breast:
4	chr1:169819577..169821810-chr1:169823722..169826124,2	K562	blood:
5	chr1:169819515..169822344-chr1:169896401..169898488,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000171806	Chromatin interaction
ENSG00000000457	Chromatin interaction
ENSG00000000460	Chromatin interaction

Extended variants
information (count: 87 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs10733054	0.80[JPT][hapmap]
rs10737549	0.93[ASW][hapmap];0.90[CHB][hapmap];0.91[CHD][hapmap];0.84[JPT][hapmap];0.84[LWK][hapmap];0.92[MKK][hapmap];0.87[YRI][hapmap];0.83[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs10737550	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10737551	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.90[YRI][hapmap];0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10800479	0.83[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs10800480	0.95[CHB][hapmap];0.90[JPT][hapmap];0.95[YRI][hapmap];0.89[ASN][1000 genomes]
rs10800481	0.95[CHB][hapmap];0.95[JPT][hapmap];0.95[YRI][hapmap];0.82[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs10800483	0.90[CHB][hapmap];0.94[CHD][hapmap];0.90[JPT][hapmap];0.87[LWK][hapmap];0.86[MEX][hapmap];0.92[MKK][hapmap];0.95[YRI][hapmap];0.82[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs10800484	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10800486	0.82[YRI][hapmap]
rs10919239	0.80[JPT][hapmap]
rs10919245	0.82[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs10919248	0.95[CHB][hapmap];0.90[JPT][hapmap];0.95[YRI][hapmap];0.83[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs10919251	0.88[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs10919257	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10919263	0.81[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs12047487	0.92[CEU][hapmap];0.81[CHB][hapmap];0.90[YRI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12133843	0.93[ASW][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.90[JPT][hapmap];0.87[LWK][hapmap];0.85[MEX][hapmap];0.97[MKK][hapmap];0.95[YRI][hapmap];0.87[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs1883436	0.87[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs2056981	0.95[CHB][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs2143122	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2179396	0.95[CHB][hapmap];0.90[JPT][hapmap];0.95[YRI][hapmap];0.87[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs2205845	0.80[YRI][hapmap]
rs2281039	0.88[ASN][1000 genomes]
rs2294322	0.87[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs2294496	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2420512	0.95[ASN][1000 genomes]
rs2901179	1.00[CHB][hapmap];0.90[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3753308	0.86[YRI][hapmap]
rs3766132	0.95[CHB][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs3766134	0.88[ASN][1000 genomes]
rs3766137	0.95[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs3766142	0.95[ASN][1000 genomes]
rs3766144	0.93[ASW][hapmap];0.96[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.95[LWK][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3766148	0.93[ASW][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.90[JPT][hapmap];0.86[LWK][hapmap];0.95[YRI][hapmap];0.83[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs3766151	0.90[CHB][hapmap];0.81[CHD][hapmap];0.95[JPT][hapmap];0.81[MEX][hapmap];0.86[ASN][1000 genomes]
rs3766154	0.89[CHB][hapmap];0.94[JPT][hapmap];0.95[YRI][hapmap];0.80[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs3766155	1.00[CEU][hapmap];0.86[YRI][hapmap];0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4376791	0.96[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs4508080	0.93[ASW][hapmap];0.90[CHB][hapmap];0.94[CHD][hapmap];0.90[JPT][hapmap];0.89[LWK][hapmap];0.86[MEX][hapmap];0.92[MKK][hapmap];0.95[YRI][hapmap];0.85[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs4614317	0.95[CHB][hapmap];0.90[JPT][hapmap];0.95[YRI][hapmap];0.81[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs4615900	0.95[CHB][hapmap];0.90[JPT][hapmap];0.95[ASN][1000 genomes]
rs4656196	0.95[CHB][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs4656197	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4656199	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4656200	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4656721	0.94[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs4656725	0.87[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs508063	0.85[CEU][hapmap]
rs603246	0.82[CEU][hapmap]
rs6427217	0.83[JPT][hapmap]
rs6427220	0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6427224	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6427225	0.93[ASW][hapmap];0.90[CHB][hapmap];0.92[CHD][hapmap];0.90[JPT][hapmap];0.89[LWK][hapmap];0.86[MEX][hapmap];0.85[MKK][hapmap];0.95[YRI][hapmap];0.88[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs6427226	0.94[CHB][hapmap];0.94[JPT][hapmap];0.81[YRI][hapmap];0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6427227	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6427228	0.88[ASN][1000 genomes]
rs6656965	0.87[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs6664099	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6668114	1.00[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6669794	0.93[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs6671752	0.89[ASN][1000 genomes]
rs6680650	0.82[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs6680938	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6682137	0.94[ASN][1000 genomes]
rs6682835	0.95[JPT][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs6683056	0.93[ASW][hapmap];0.84[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap];0.81[MEX][hapmap];0.82[MKK][hapmap];0.95[YRI][hapmap];0.84[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs6684481	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6687377	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.95[MEX][hapmap];0.98[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6702969	0.86[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs717481	0.87[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs732185	0.90[CHB][hapmap];0.83[JPT][hapmap];0.94[ASN][1000 genomes]
rs7519364	0.89[ASN][1000 genomes]
rs7521700	0.87[ASW][hapmap];1.00[CEU][hapmap];0.81[LWK][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.80[YRI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7525259	0.93[ASW][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.90[JPT][hapmap];0.89[LWK][hapmap];0.86[MEX][hapmap];0.92[MKK][hapmap];0.95[YRI][hapmap];0.88[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs7530237	0.93[ASW][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.90[JPT][hapmap];0.92[LWK][hapmap];0.93[MKK][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs7545011	0.81[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs9287097	0.93[ASW][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.90[JPT][hapmap];0.89[LWK][hapmap];0.86[MEX][hapmap];0.92[MKK][hapmap];0.95[YRI][hapmap];0.87[AFR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3451367	chr1:169630075-169976964	Strong transcription Flanking Active TSS Genic enhancers Enhancers Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	esv1814601	chr1:169782006-169885186	Weak transcription Active TSS Flanking Active TSS Enhancers Strong 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	23 gene(s)	inside rSNPs	diseases
3	esv1821503	chr1:169782006-169885186	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	esv1847722	chr1:169782006-169885186	Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
5	esv2757760	chr1:169782006-169885186	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
6	esv2758976	chr1:169782006-169885186	Strong transcription Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
7	nsv428268	chr1:169782006-169885186	Strong transcription ZNF genes & repeats Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
8	esv1845220	chr1:169782006-169933886	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
9	nsv872542	chr1:169802760-169844093	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4656724	C1orf156	cis	parietal	SCAN
rs4656724	TADA1	cis	cerebellum	SCAN
rs4656724	SCYL3	cis	cerebellum	SCAN
rs4656724	C1orf156	cis	cerebellum	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169764800-169823600	Weak transcription	Gastric	stomach
2	chr1:169765000-169821800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr1:169765200-169823400	Weak transcription	Right Ventricle	heart
4	chr1:169765400-169822600	Weak transcription	Colonic Mucosa	Colon
5	chr1:169786200-169862400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr1:169786600-169841400	Strong transcription	Dnd41	blood
7	chr1:169788600-169823600	Weak transcription	Pancreas	Pancrea
8	chr1:169791200-169841200	Strong transcription	Fetal Thymus	thymus
9	chr1:169793800-169822600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr1:169794800-169822000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr1:169802200-169822600	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr1:169802400-169821800	Weak transcription	Colon Smooth Muscle	Colon
13	chr1:169805400-169848800	Strong transcription	Monocytes-CD14+_RO01746	blood
14	chr1:169806600-169860000	Weak transcription	Stomach Mucosa	stomach
15	chr1:169808200-169822000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr1:169808200-169841200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr1:169808600-169821800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr1:169808600-169827000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr1:169808800-169823200	Weak transcription	Fetal Heart	heart
20	chr1:169809200-169829400	Strong transcription	GM12878-XiMat	blood
21	chr1:169809200-169829600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr1:169810000-169828000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
23	chr1:169810400-169841400	Strong transcription	HUES48 Cell Line	embryonic stem cell
24	chr1:169810600-169841200	Strong transcription	Primary monocytes fromperipheralblood	blood
25	chr1:169810800-169841000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr1:169810800-169841200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr1:169811000-169841400	Strong transcription	Rectal Mucosa Donor 29	rectum
28	chr1:169811400-169825600	Strong transcription	HSMM	muscle
29	chr1:169811400-169827200	Strong transcription	K562	blood
30	chr1:169811600-169841200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
31	chr1:169811800-169827600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr1:169811800-169836200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr1:169811800-169841400	Strong transcription	HUES64 Cell Line	embryonic stem cell
34	chr1:169812000-169840800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr1:169812800-169836400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr1:169813000-169822600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr1:169813400-169841200	Strong transcription	Fetal Intestine Large	intestine
38	chr1:169814200-169838000	Strong transcription	Placenta	Placenta
39	chr1:169814400-169830400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr1:169814400-169848600	Strong transcription	Duodenum Mucosa	Duodenum
41	chr1:169814600-169843200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr1:169814800-169836000	Strong transcription	Osteobl	bone
43	chr1:169814800-169848000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr1:169815000-169845200	Strong transcription	Rectal Mucosa Donor 31	rectum
45	chr1:169815200-169822000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
46	chr1:169815200-169843000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
47	chr1:169815200-169848200	Strong transcription	Primary T helper cells PMA-I stimulated	--
48	chr1:169815400-169848400	Strong transcription	Primary T helper cells fromperipheralblood	blood
49	chr1:169816600-169827800	Strong transcription	NHDF-Ad	bronchial
50	chr1:169817000-169826000	Strong transcription	iPS-18 Cell Line	embryonic stem cell

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