Variant report

Variant	rs1218598
Chromosome Location	chr1:154795389-154795390
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:154793548..154796604-chr1:154817553..154820667,3	MCF-7	breast:
2	chr1:154792210..154794358-chr1:154794481..154796259,2	MCF-7	breast:
3	chr1:154792841..154796481-chr1:154806032..154808624,3	MCF-7	breast:
4	chr1:154783206..154790651-chr1:154790786..154795764,8	K562	blood:

Extended variants
information (count: 12 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs1010225	0.87[CEU][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs1218551	1.00[JPT][hapmap];0.83[MEX][hapmap];0.82[ASN][1000 genomes]
rs1218552	0.84[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs1218553	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2798604	1.00[JPT][hapmap];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948413	chr1:153974621-154797272	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	132 gene(s)	inside rSNPs	diseases
2	nsv532579	chr1:154548165-155262692	Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	575 gene(s)	inside rSNPs	diseases
3	nsv427797	chr1:154559115-154933717	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
4	nsv470740	chr1:154568683-154796895	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS 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	18 gene(s)	inside rSNPs	diseases
5	nsv464050	chr1:154568683-154801247	Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
6	nsv547958	chr1:154568683-154801247	Enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
7	nsv432931	chr1:154794318-154855055	Weak transcription Flanking Bivalent TSS/Enh Enhancers Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs1218598	RAG1AP1	cis	parietal	SCAN
rs1218598	SNAPIN	cis	parietal	SCAN
rs1218598	RXFP4	cis	cerebellum	SCAN
rs1218598	LCE3C	cis	parietal	SCAN
rs1218598	SETDB1	cis	cerebellum	SCAN
rs1218598	S100A1	cis	parietal	SCAN
rs1218598	OTUD7B	cis	parietal	SCAN

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:154786600-154801800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr1:154787000-154795600	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr1:154787000-154800400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr1:154787000-154805400	Weak transcription	Brain Cingulate Gyrus	brain
5	chr1:154792200-154796000	Enhancers	Colon Smooth Muscle	Colon
6	chr1:154792800-154800200	Weak transcription	Gastric	stomach
7	chr1:154792800-154805800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr1:154793200-154796800	Weak transcription	Psoas Muscle	Psoas
9	chr1:154793400-154796000	Weak transcription	Right Atrium	heart
10	chr1:154793600-154803600	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr1:154793800-154797800	Enhancers	Fetal Muscle Leg	muscle
12	chr1:154794200-154795400	Weak transcription	Stomach Smooth Muscle	stomach
13	chr1:154794200-154796600	Enhancers	Fetal Muscle Trunk	muscle
14	chr1:154794400-154795800	Enhancers	H1 Cell Line	embryonic stem cell
15	chr1:154794400-154795800	Enhancers	HSMMtube	muscle
16	chr1:154794400-154799600	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr1:154794600-154795600	Enhancers	iPS-18 Cell Line	embryonic stem cell
18	chr1:154794600-154795600	Enhancers	Brain Germinal Matrix	brain
19	chr1:154794600-154795600	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr1:154794600-154797400	Enhancers	Fetal Brain Female	brain
21	chr1:154794600-154797800	Enhancers	Fetal Brain Male	brain
22	chr1:154794600-154797800	Enhancers	Fetal Stomach	stomach
23	chr1:154794600-154802800	Weak transcription	Right Ventricle	heart
24	chr1:154794800-154795400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr1:154794800-154795600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr1:154794800-154795600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr1:154794800-154795800	Enhancers	ES-I3 Cell Line	embryonic stem cell
28	chr1:154794800-154797800	Enhancers	GM12878-XiMat	blood
29	chr1:154795000-154795400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
30	chr1:154795000-154795400	Enhancers	Ovary	ovary
31	chr1:154795000-154795600	Enhancers	iPS-20b Cell Line	embryonic stem cell
32	chr1:154795000-154795600	Enhancers	Duodenum Mucosa	Duodenum
33	chr1:154795200-154795400	Enhancers	Brain Anterior Caudate	brain
34	chr1:154795200-154795400	Enhancers	Brain Hippocampus Middle	brain
35	chr1:154795200-154795600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr1:154795200-154796000	Enhancers	HUES6 Cell Line	embryonic stem cell

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