Variant report

Variant	rs4636463
Chromosome Location	chr1:151233080-151233081
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:151226179..151229038-chr1:151231649..151233536,2	K562	blood:
2	chr1:151232549..151234323-chr1:151235189..151237747,2	MCF-7	breast:
3	1:151219411-151234038..1:151592347-151603110	K562	blood:
4	1:151171193-151178589..1:151219411-151234038	GM12878	blood:
5	chr1:151231717..151234446-chr1:151235033..151237516,2	K562	blood:
6	chr1:151225633..151229215-chr1:151231593..151235514,4	MCF-7	breast:
7	chr1:151231517..151234313-chr1:151236642..151238843,2	K562	blood:
8	chr1:151232097..151234568-chr1:151249498..151251245,2	MCF-7	breast:
9	chr1:151230341..151233216-chr1:151253682..151256078,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000143373	Chromatin interaction
ENSG00000232671	Chromatin interaction
ENSG00000143398	Chromatin interaction
ENSG00000159352	Chromatin interaction
ENSG00000206635	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs1056847	0.90[JPT][hapmap]
rs10749660	0.90[GIH][hapmap];0.85[JPT][hapmap]
rs10788801	1.00[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.80[TSI][hapmap];0.88[YRI][hapmap];0.86[ASN][1000 genomes]
rs10788803	0.90[JPT][hapmap]
rs10888408	0.90[GIH][hapmap];0.90[JPT][hapmap]
rs10888409	0.90[JPT][hapmap]
rs10888410	0.90[JPT][hapmap]
rs11204785	0.90[GIH][hapmap];0.85[JPT][hapmap]
rs11204791	0.90[GIH][hapmap];0.90[JPT][hapmap]
rs11589120	0.85[ASN][1000 genomes]
rs1536617	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs16827941	0.83[JPT][hapmap]
rs1752387	0.95[JPT][hapmap]
rs1892196	0.90[GIH][hapmap]
rs2025900	0.90[JPT][hapmap]
rs2031797	0.88[CHB][hapmap];0.86[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes]
rs2275900	0.90[GIH][hapmap];0.90[JPT][hapmap]
rs2769267	0.81[JPT][hapmap]
rs2769268	0.90[JPT][hapmap]
rs2769273	0.90[JPT][hapmap]
rs2800946	0.90[JPT][hapmap]
rs3811405	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.94[LWK][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap]
rs3811406	0.88[CHB][hapmap];0.92[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4246525	0.85[JPT][hapmap]
rs4520422	0.90[GIH][hapmap];0.84[JPT][hapmap]
rs4970944	0.92[GIH][hapmap];0.85[JPT][hapmap]
rs4970948	0.90[JPT][hapmap]
rs4971013	0.92[GIH][hapmap];0.84[JPT][hapmap]
rs4971017	0.81[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs4971018	1.00[ASW][hapmap];0.83[CHB][hapmap];0.84[JPT][hapmap];1.00[LWK][hapmap];0.93[YRI][hapmap];0.85[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs4971023	0.85[JPT][hapmap]
rs4971027	0.90[JPT][hapmap]
rs4971028	0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4971029	0.88[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes]
rs4971030	0.90[JPT][hapmap]
rs5022636	0.81[JPT][hapmap]
rs6587559	0.92[GIH][hapmap];0.85[JPT][hapmap]
rs6587562	0.90[JPT][hapmap]
rs6678528	1.00[ASW][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.85[YRI][hapmap];0.85[ASN][1000 genomes]
rs6686402	0.90[GIH][hapmap];0.85[JPT][hapmap]
rs6695344	0.88[GIH][hapmap]
rs6702612	0.87[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs7527032	0.90[GIH][hapmap];0.85[JPT][hapmap]
rs7532935	0.90[GIH][hapmap];0.85[JPT][hapmap]
rs7539584	0.90[GIH][hapmap];0.85[JPT][hapmap]
rs7544947	0.92[GIH][hapmap];0.85[JPT][hapmap]
rs7545024	0.89[ASN][1000 genomes]
rs7545392	0.86[JPT][hapmap]
rs7552226	0.86[ASW][hapmap];0.89[LWK][hapmap];0.81[YRI][hapmap]
rs7552906	0.86[JPT][hapmap]
rs943637	0.90[JPT][hapmap]

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	nsv1001897	chr1:150743271-151241600	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
2	nsv535158	chr1:150743271-151241600	Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
3	nsv522840	chr1:150933723-151347746	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	169 gene(s)	inside rSNPs	diseases
4	nsv916272	chr1:150961809-151557253	Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	219 gene(s)	inside rSNPs	diseases
5	nsv831559	chr1:151109459-151239921	Active TSS Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
6	nsv831570	chr1:151129020-151281778	Strong transcription Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	106 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs4636463	RFX5	cis	cerebellum	SCAN
rs4636463	PSMD4	cis	parietal	SCAN
rs4636463	CTSS	cis	cerebellum	SCAN
rs4636463	HORMAD1	cis	parietal	SCAN
rs4636463	PSMD4	cis	cerebellum	SCAN
rs4636463	FLG	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151227600-151236200	Weak transcription	Spleen	Spleen
2	chr1:151228000-151234600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr1:151228000-151236200	Weak transcription	Gastric	stomach
4	chr1:151228200-151234600	Weak transcription	Ovary	ovary
5	chr1:151228200-151236400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr1:151228200-151237000	Weak transcription	Fetal Kidney	kidney
7	chr1:151228400-151234200	Weak transcription	Fetal Thymus	thymus
8	chr1:151228400-151234400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr1:151228400-151234400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr1:151228400-151234400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr1:151228400-151234400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr1:151228400-151234400	Weak transcription	Thymus	Thymus
13	chr1:151228400-151234600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr1:151228400-151234600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr1:151228400-151234600	Weak transcription	Primary B cells from peripheral blood	blood
16	chr1:151228400-151234600	Weak transcription	Brain Hippocampus Middle	brain
17	chr1:151228400-151234600	Weak transcription	Brain Substantia Nigra	brain
18	chr1:151228400-151234600	Weak transcription	Fetal Brain Female	brain
19	chr1:151228400-151234600	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr1:151228400-151234600	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr1:151228400-151234600	Weak transcription	Rectal Smooth Muscle	rectum
22	chr1:151228400-151234800	Weak transcription	Colonic Mucosa	Colon
23	chr1:151228400-151234800	Weak transcription	Fetal Intestine Large	intestine
24	chr1:151228400-151236200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr1:151228400-151236200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr1:151228400-151236400	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr1:151228400-151236400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr1:151228400-151236400	Weak transcription	Aorta	Aorta
29	chr1:151228400-151236400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr1:151228400-151236400	Weak transcription	HSMMtube	muscle
31	chr1:151228400-151236400	Weak transcription	NHDF-Ad	bronchial
32	chr1:151228400-151236600	Weak transcription	Pancreas	Pancrea
33	chr1:151228400-151238200	Weak transcription	Small Intestine	intestine
34	chr1:151228400-151238400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr1:151228400-151244000	Weak transcription	Right Atrium	heart
36	chr1:151228400-151253400	Weak transcription	Fetal Brain Male	brain
37	chr1:151228600-151233800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr1:151228600-151234000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr1:151228600-151234000	Weak transcription	Primary monocytes fromperipheralblood	blood
40	chr1:151228600-151234000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
41	chr1:151228600-151234000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr1:151228600-151234200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
43	chr1:151228600-151234200	Weak transcription	Fetal Muscle Leg	muscle
44	chr1:151228600-151234400	Weak transcription	HUES48 Cell Line	embryonic stem cell
45	chr1:151228600-151234400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
46	chr1:151228600-151234400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr1:151228600-151234400	Weak transcription	Adipose Nuclei	Adipose
48	chr1:151228600-151234400	Weak transcription	Brain Cingulate Gyrus	brain
49	chr1:151228600-151234400	Weak transcription	Brain Germinal Matrix	brain
50	chr1:151228600-151234600	Weak transcription	HUES6 Cell Line	embryonic stem cell

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