Variant report

Variant	rs9865
Chromosome Location	chr1:46827456-46827457
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:46804000..46807953-chr1:46827356..46830611,4	K562	blood:
2	chr1:46815399..46818374-chr1:46824633..46827499,2	K562	blood:
3	chr1:46806380..46807953-chr1:46827356..46829376,2	K562	blood:
4	chr1:46826155..46827857-chr1:46834511..46836934,2	K562	blood:
5	chr1:46817441..46820016-chr1:46826490..46829011,2	K562	blood:

Variant related genes	Relation type
ENSG00000117481	Chromatin interaction
ENSG00000225779	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10252	0.91[CHB][hapmap];0.89[CHD][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs1048771	0.86[CHD][hapmap]
rs11211271	0.80[CHB][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs11542623	0.81[CHB][hapmap];0.86[CHD][hapmap];0.86[MEX][hapmap]
rs11802866	0.85[ASN][1000 genomes]
rs11804189	0.91[ASN][1000 genomes]
rs12073998	0.82[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs12075550	0.91[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs12562440	0.85[ASN][1000 genomes]
rs12563610	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs17102101	0.81[CHB][hapmap];0.86[CHD][hapmap];0.86[MEX][hapmap]
rs2145409	0.85[ASN][1000 genomes]
rs2295464	0.81[CHB][hapmap]
rs2295465	0.81[CHB][hapmap];0.88[CHD][hapmap];0.82[MEX][hapmap];0.85[TSI][hapmap]
rs324416	0.83[ASN][1000 genomes]
rs3753362	0.81[CHB][hapmap];0.89[CHD][hapmap];0.86[MEX][hapmap]
rs3766248	0.81[CHB][hapmap]
rs3863641	0.85[CHB][hapmap];0.89[CHD][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs3891758	0.95[AFR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4110477	0.90[AFR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs41293281	0.90[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs41294484	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs45480993	0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs45540335	0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs45564237	0.83[ASN][1000 genomes]
rs45577432	0.84[ASN][1000 genomes]
rs4660345	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs4660925	0.84[ASN][1000 genomes]
rs5013328	0.84[ASN][1000 genomes]
rs56733721	0.91[ASN][1000 genomes]
rs58710660	0.98[ASN][1000 genomes]
rs59082884	1.00[AFR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59411358	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs60519942	0.98[ASN][1000 genomes]
rs61221162	1.00[ASN][1000 genomes]
rs61784604	0.90[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs873978	0.80[CHB][hapmap];0.89[CHD][hapmap];0.88[JPT][hapmap];0.83[ASN][1000 genomes]
rs913168	0.81[CHB][hapmap];0.88[JPT][hapmap];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005189	chr1:46335186-46949309	Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv534946	chr1:46335186-46949309	ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
3	esv2761743	chr1:46339858-47026743	Active TSS Weak transcription Bivalent Enhancer Enhancers Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
4	nsv829748	chr1:46724508-46876122	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
5	nsv546162	chr1:46807597-46870761	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs9865	FAAH	cis	cerebellum	SCAN
rs9865	RAD54L	cis	cerebellum	SCAN
rs9865	C1orf223	cis	parietal	SCAN
rs9865	C1orf228	cis	parietal	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:46807200-46827600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr1:46807400-46831800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr1:46807400-46832200	Strong transcription	Fetal Stomach	stomach
4	chr1:46807600-46835400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr1:46807600-46844600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr1:46807800-46835000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr1:46808600-46831800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr1:46808600-46834600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
9	chr1:46809200-46831600	Strong transcription	HUES6 Cell Line	embryonic stem cell
10	chr1:46809200-46848600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr1:46810200-46831600	Strong transcription	Fetal Thymus	thymus
12	chr1:46810400-46832800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr1:46812400-46830600	Strong transcription	Fetal Intestine Large	intestine
14	chr1:46812600-46835200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr1:46813000-46835000	Strong transcription	Fetal Muscle Trunk	muscle
16	chr1:46813400-46834600	Strong transcription	Fetal Intestine Small	intestine
17	chr1:46814000-46830800	Strong transcription	Primary T helper cells PMA-I stimulated	--
18	chr1:46814200-46830200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr1:46814200-46834800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr1:46814600-46834400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr1:46815000-46831600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr1:46815000-46831600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr1:46815200-46835000	Strong transcription	Liver	Liver
24	chr1:46815200-46835200	Strong transcription	Primary T cells fromperipheralblood	blood
25	chr1:46816800-46835800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr1:46817800-46829400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr1:46818000-46829400	Strong transcription	Cortex derived primary cultured neurospheres	brain
28	chr1:46818000-46831000	Strong transcription	HUES64 Cell Line	embryonic stem cell
29	chr1:46818000-46834800	Strong transcription	Lung	lung
30	chr1:46818200-46829600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr1:46818200-46832000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr1:46818200-46834800	Strong transcription	Duodenum Mucosa	Duodenum
33	chr1:46818200-46834800	Strong transcription	Osteobl	bone
34	chr1:46818200-46839400	Strong transcription	Dnd41	blood
35	chr1:46820200-46834800	Strong transcription	Duodenum Smooth Muscle	Duodenum
36	chr1:46820800-46829800	Strong transcription	HUVEC	blood vessel
37	chr1:46822200-46829000	Strong transcription	H9 Cell Line	embryonic stem cell
38	chr1:46822200-46835800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
39	chr1:46823000-46830400	Strong transcription	NHEK	skin
40	chr1:46823000-46834600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr1:46823400-46831600	Strong transcription	Monocytes-CD14+_RO01746	blood
42	chr1:46824000-46829800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr1:46824400-46829200	Strong transcription	Brain Cingulate Gyrus	brain
44	chr1:46824400-46829400	Strong transcription	NH-A	brain
45	chr1:46824400-46831000	Strong transcription	Stomach Smooth Muscle	stomach
46	chr1:46824400-46831200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr1:46824400-46831400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr1:46824400-46831800	Strong transcription	Primary monocytes fromperipheralblood	blood
49	chr1:46824600-46829200	Strong transcription	Brain Anterior Caudate	brain
50	chr1:46824600-46829200	Strong transcription	Colon Smooth Muscle	Colon

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