Variant report

Variant	rs284878
Chromosome Location	chr1:92174260-92174261
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:92172545..92174973-chr1:92176760..92181587,6	K562	blood:
2	chr1:92169004..92174919-chr1:92176719..92181810,13	K562	blood:
3	chr1:92171556..92174319-chr1:92192044..92194001,2	K562	blood:

Variant related genes	Relation type
ENSG00000069702	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs1012069	0.88[CHB][hapmap];0.84[CHD][hapmap]
rs10157635	0.81[CHB][hapmap];0.87[CHD][hapmap];0.90[TSI][hapmap];0.93[EUR][1000 genomes]
rs10157887	0.82[CHB][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10874909	0.83[CHB][hapmap];0.81[CHD][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11165347	0.89[CHB][hapmap]
rs12060235	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12065370	0.88[CHB][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1542703	0.89[CHB][hapmap];0.87[CHD][hapmap]
rs1613413	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17131536	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.90[TSI][hapmap];0.87[YRI][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17131541	0.89[CHB][hapmap];0.81[CHD][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2810889	0.88[CHB][hapmap];0.82[JPT][hapmap];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2810890	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs284866	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs284867	0.87[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs284868	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[MEX][hapmap];0.90[TSI][hapmap];0.87[YRI][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs284869	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs284871	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs284872	0.86[ASN][1000 genomes]
rs284875	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs284877	1.00[CHB][hapmap];0.97[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009560	chr1:91897078-92270781	Enhancers Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv1012864	chr1:92067100-92827761	Flanking Active TSS Strong transcription Enhancers Active TSS Weak transcription Genic enhancers ZNF genes & repeats 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	33 gene(s)	inside rSNPs	diseases
3	nsv535029	chr1:92067100-92827761	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	esv2763581	chr1:92068967-92203803	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
5	nsv1014990	chr1:92084142-92206674	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
6	nsv530438	chr1:92091957-92827760	Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
7	nsv1010179	chr1:92140209-92655952	Weak transcription Genic enhancers Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats 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	19 gene(s)	inside rSNPs	diseases
8	nsv535030	chr1:92140209-92655952	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:92152600-92184200	Strong transcription	HepG2	liver
2	chr1:92153000-92197000	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr1:92155400-92178800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr1:92155600-92178800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr1:92155800-92191200	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr1:92156200-92177800	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr1:92159800-92183800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
8	chr1:92163200-92176800	Weak transcription	Duodenum Mucosa	Duodenum
9	chr1:92164000-92184400	Weak transcription	Hela-S3	cervix
10	chr1:92164000-92195000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr1:92164200-92175000	Weak transcription	GM12878-XiMat	blood
12	chr1:92164200-92176000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr1:92164800-92177800	Weak transcription	Primary T helper cells fromperipheralblood	blood
14	chr1:92165200-92177400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
15	chr1:92165400-92178600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr1:92165400-92178600	Weak transcription	Fetal Brain Male	brain
17	chr1:92165600-92175400	Strong transcription	Stomach Smooth Muscle	stomach
18	chr1:92165800-92184800	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr1:92165800-92196800	Weak transcription	Small Intestine	intestine
20	chr1:92166600-92191000	Weak transcription	Brain Hippocampus Middle	brain
21	chr1:92167400-92184800	Weak transcription	A549	lung
22	chr1:92167800-92178000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr1:92167800-92178200	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr1:92168000-92178600	Weak transcription	Osteobl	bone
25	chr1:92168000-92191000	Weak transcription	HUVEC	blood vessel
26	chr1:92169200-92178800	Strong transcription	Liver	Liver
27	chr1:92169800-92187200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr1:92170000-92176000	Strong transcription	Adipose Nuclei	Adipose
29	chr1:92170000-92177600	Enhancers	Fetal Heart	heart
30	chr1:92170400-92174600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr1:92170400-92175200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr1:92170400-92176200	Strong transcription	NHDF-Ad	bronchial
33	chr1:92170400-92176800	Strong transcription	Fetal Stomach	stomach
34	chr1:92171000-92196800	Weak transcription	Rectal Mucosa Donor 31	rectum
35	chr1:92171200-92196800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr1:92171600-92174600	Strong transcription	Lung	lung
37	chr1:92171600-92176400	Strong transcription	Ovary	ovary
38	chr1:92171800-92174400	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
39	chr1:92171800-92174400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr1:92171800-92178600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
41	chr1:92172200-92174600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
42	chr1:92172200-92174800	Strong transcription	Duodenum Smooth Muscle	Duodenum
43	chr1:92172200-92178600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr1:92172200-92178600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr1:92172200-92178600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr1:92172400-92174600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr1:92172400-92178000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr1:92172600-92174600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
49	chr1:92172600-92178200	Strong transcription	Fetal Intestine Large	intestine
50	chr1:92172800-92174400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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