Variant report

Variant	rs1281415
Chromosome Location	chr1:179827381-179827382
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:179826273..179829701-chr1:179831167..179834535,5	K562	blood:
2	chr1:179809907..179811808-chr1:179827291..179829584,2	MCF-7	breast:
3	chr1:179820647..179822358-chr1:179825151..179827760,2	K562	blood:
4	chr1:179826227..179827914-chr1:179850266..179853011,2	MCF-7	breast:
5	chr1:179784112..179785710-chr1:179826992..179828594,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000258664	Chromatin interaction
ENSG00000143337	Chromatin interaction
ENSG00000272906	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1148813	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1148814	1.00[CEU][hapmap];0.82[CHB][hapmap];0.86[JPT][hapmap];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1148816	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1148818	0.87[ASN][1000 genomes]
rs1281409	0.89[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1281414	0.95[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs1281419	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1281424	0.87[ASN][1000 genomes]
rs1281425	1.00[CHB][hapmap];0.89[CHD][hapmap];0.89[JPT][hapmap];0.87[ASN][1000 genomes]
rs1281431	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.84[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1290274	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1295972	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1299683	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1299685	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17370666	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1758143	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2762857	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2777907	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2777916	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2794584	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs476280	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs524166	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs555755	0.94[EUR][1000 genomes]
rs576723	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs627897	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs651455	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs668813	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs683812	1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005808	chr1:179783922-179864710	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
2	nsv1005051	chr1:179785643-179861950	Flanking Active TSS Strong transcription Genic enhancers Weak transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
3	nsv429936	chr1:179790343-180214343	Active TSS Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
4	nsv429947	chr1:179790518-179925104	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
5	esv1815608	chr1:179813499-180067988	Strong transcription Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers ZNF genes & repeats 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	48 gene(s)	inside rSNPs	diseases
6	nsv429958	chr1:179814306-179994628	Genic enhancers Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:179795600-179834200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr1:179802400-179836200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr1:179803600-179833600	Weak transcription	Fetal Brain Male	brain
4	chr1:179807600-179827400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr1:179807800-179833800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr1:179808600-179837000	Strong transcription	Liver	Liver
7	chr1:179808600-179839800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr1:179808800-179836000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr1:179809800-179827800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr1:179810200-179828000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr1:179812200-179827800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr1:179812600-179842600	Weak transcription	Stomach Mucosa	stomach
13	chr1:179813200-179839200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr1:179813400-179834000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr1:179814200-179834400	Weak transcription	Fetal Heart	heart
16	chr1:179814400-179839200	Strong transcription	HSMM	muscle
17	chr1:179815000-179828400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr1:179815000-179839400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr1:179816000-179836000	Weak transcription	Colonic Mucosa	Colon
20	chr1:179820200-179829600	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr1:179820200-179831600	Weak transcription	Esophagus	oesophagus
22	chr1:179820200-179834200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr1:179820400-179829200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr1:179820400-179829800	Weak transcription	Psoas Muscle	Psoas
25	chr1:179820400-179831600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
26	chr1:179820400-179832200	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr1:179820400-179833600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
28	chr1:179820400-179834000	Weak transcription	Brain Cingulate Gyrus	brain
29	chr1:179820400-179841400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
30	chr1:179820400-179841800	Weak transcription	Small Intestine	intestine
31	chr1:179820400-179844200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr1:179820400-179845400	Weak transcription	Right Ventricle	heart
33	chr1:179820600-179831000	Weak transcription	H1 Cell Line	embryonic stem cell
34	chr1:179820600-179832600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
35	chr1:179820600-179832800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr1:179820600-179834000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
37	chr1:179820600-179834000	Weak transcription	HSMMtube	muscle
38	chr1:179821000-179827800	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr1:179821000-179830200	Weak transcription	GM12878-XiMat	blood
40	chr1:179821000-179833400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
41	chr1:179821000-179833600	Weak transcription	H9 Cell Line	embryonic stem cell
42	chr1:179821000-179833600	Weak transcription	Fetal Kidney	kidney
43	chr1:179821000-179834200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr1:179821200-179832400	Weak transcription	Primary T helper cells PMA-I stimulated	--
45	chr1:179821200-179834000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
46	chr1:179821400-179830000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr1:179821800-179832600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
48	chr1:179822000-179827600	Weak transcription	Hela-S3	cervix
49	chr1:179822000-179829800	Weak transcription	Rectal Mucosa Donor 31	rectum
50	chr1:179822000-179830800	Weak transcription	HUVEC	blood vessel

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