Variant report

Variant	rs11802358
Chromosome Location	chr1:227085155-227085156
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:227076139..227079788-chr1:227081535..227086284,4	K562	blood:

Variant related genes	Relation type
ENSG00000143801	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1046240	0.90[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs1150897	0.83[ASN][1000 genomes]
rs1150900	0.95[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs1295638	0.90[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs1295640	0.90[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.81[LWK][hapmap]
rs1295641	0.88[ASN][1000 genomes]
rs1295643	0.88[ASN][1000 genomes]
rs1295647	0.80[ASN][1000 genomes]
rs1296171	0.81[ASN][1000 genomes]
rs2073489	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2236914	0.95[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs2236915	0.95[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs2793461	0.88[ASN][1000 genomes]
rs2802268	0.83[ASW][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.95[YRI][hapmap];0.91[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs2855559	0.96[ASN][1000 genomes]
rs2855560	0.96[ASN][1000 genomes]
rs2855564	0.96[ASN][1000 genomes]
rs4653470	0.94[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs6426547	0.83[ASN][1000 genomes]
rs6426548	0.83[ASN][1000 genomes]
rs6674701	0.83[ASN][1000 genomes]
rs6688068	0.83[ASN][1000 genomes]
rs6692729	0.83[ASN][1000 genomes]
rs6697001	0.84[ASN][1000 genomes]
rs6697431	0.84[ASN][1000 genomes]
rs6759	0.90[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.82[LWK][hapmap];0.88[ASN][1000 genomes]
rs7514364	0.82[ASN][1000 genomes]
rs7518926	0.83[ASN][1000 genomes]
rs7530245	0.80[ASN][1000 genomes]
rs7530370	0.83[ASN][1000 genomes]
rs7547071	0.84[ASN][1000 genomes]
rs8383	0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003656	chr1:227034700-227559665	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer 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	35 gene(s)	inside rSNPs	diseases
2	nsv535318	chr1:227034700-227559665	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer 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	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs11802358	CABC1	cis	cerebellum	SCAN
rs11802358	ARF1	cis	cerebellum	SCAN
rs11802358	PSEN2	cis	cerebellum	SCAN
rs11802358	C1orf95	cis	cerebellum	SCAN
rs11802358	LEFTY1	cis	cerebellum	SCAN
rs11802358	HIST3H2BB	cis	parietal	SCAN
rs11802358	PARP1	cis	cerebellum	SCAN
rs11802358	SUSD4	cis	parietal	SCAN
rs11802358	PSEN2	cis	lymphoblastoid	seeQTL

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227059800-227095000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr1:227069400-227087800	Weak transcription	HMEC	breast
3	chr1:227069400-227102800	Weak transcription	K562	blood
4	chr1:227070800-227088200	Weak transcription	Fetal Brain Male	brain
5	chr1:227071000-227089000	Strong transcription	Stomach Smooth Muscle	stomach
6	chr1:227071200-227086800	Weak transcription	NHDF-Ad	bronchial
7	chr1:227071200-227088400	Weak transcription	Hela-S3	cervix
8	chr1:227071200-227091400	Weak transcription	Osteobl	bone
9	chr1:227071600-227087000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr1:227071800-227102400	Weak transcription	Small Intestine	intestine
11	chr1:227072200-227087000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr1:227072200-227091800	Weak transcription	Fetal Kidney	kidney
13	chr1:227072200-227100400	Weak transcription	Stomach Mucosa	stomach
14	chr1:227073000-227085200	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr1:227073400-227088600	Strong transcription	Fetal Stomach	stomach
16	chr1:227073400-227092200	Strong transcription	Pancreas	Pancrea
17	chr1:227073800-227100600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr1:227074200-227091800	Weak transcription	Fetal Heart	heart
19	chr1:227074800-227090000	Weak transcription	Primary B cells from peripheral blood	blood
20	chr1:227074800-227090200	Strong transcription	Duodenum Smooth Muscle	Duodenum
21	chr1:227075000-227085400	Strong transcription	Ovary	ovary
22	chr1:227075000-227087400	Weak transcription	Primary B cells from cord blood	blood
23	chr1:227075000-227088800	Strong transcription	HUES6 Cell Line	embryonic stem cell
24	chr1:227075200-227087000	Weak transcription	GM12878-XiMat	blood
25	chr1:227075200-227091800	Weak transcription	Right Atrium	heart
26	chr1:227075400-227088800	Strong transcription	Liver	Liver
27	chr1:227075600-227088200	Strong transcription	Brain Inferior Temporal Lobe	brain
28	chr1:227076600-227087400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr1:227077800-227085400	Strong transcription	Rectal Smooth Muscle	rectum
30	chr1:227078600-227091600	Weak transcription	Primary hematopoietic stem cells	blood
31	chr1:227079000-227087200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr1:227079800-227097200	Weak transcription	Brain Germinal Matrix	brain
33	chr1:227080000-227094800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr1:227080200-227087200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr1:227080200-227090600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr1:227080400-227085200	Weak transcription	Primary monocytes fromperipheralblood	blood
37	chr1:227080400-227087400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr1:227080400-227088200	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr1:227080400-227090000	Weak transcription	Pancreatic Islets	Pancreatic Islet
40	chr1:227080600-227087400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr1:227080600-227088400	Strong transcription	Left Ventricle	heart
42	chr1:227080600-227088800	Strong transcription	Adipose Nuclei	Adipose
43	chr1:227080600-227089000	Strong transcription	Skeletal Muscle Male	skeletal muscle
44	chr1:227080600-227089800	Strong transcription	Fetal Muscle Trunk	muscle
45	chr1:227080800-227093600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr1:227081000-227085600	Strong transcription	Fetal Intestine Large	intestine
47	chr1:227081000-227088800	Strong transcription	Fetal Muscle Leg	muscle
48	chr1:227081600-227087200	Weak transcription	H1 Cell Line	embryonic stem cell
49	chr1:227081800-227089200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
50	chr1:227082000-227085400	Strong transcription	Brain Angular Gyrus	brain

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