Variant report

Variant	rs324702
Chromosome Location	chr4:76737790-76737791
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:76593006..76595820-chr4:76737546..76740383,2	K562	blood:

Extended variants
information (count: 29 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10031532	1.00[CEU][hapmap];0.91[YRI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13119659	0.94[AFR][1000 genomes]
rs17000786	0.87[TSI][hapmap]
rs28541901	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs324687	1.00[CEU][hapmap];0.91[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs324690	0.87[TSI][hapmap]
rs324694	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs324704	0.91[YRI][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs324705	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs324706	1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[MKK][hapmap];0.85[TSI][hapmap]
rs324710	1.00[CEU][hapmap];0.91[YRI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs324720	0.84[CEU][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs324726	0.87[TSI][hapmap]
rs324727	0.87[TSI][hapmap]
rs324729	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs324734	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs324735	0.87[TSI][hapmap]
rs324736	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs324739	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs324740	0.87[TSI][hapmap]
rs41398350	1.00[CHD][hapmap]
rs4262008	0.83[TSI][hapmap]
rs55884734	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6817228	0.82[EUR][1000 genomes]
rs6823013	1.00[CHD][hapmap]
rs6841486	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7691515	0.95[AMR][1000 genomes];0.93[EUR][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	esv3353539	chr4:76530136-76993859	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS 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	51 gene(s)	inside rSNPs	diseases
2	nsv529613	chr4:76654941-77081576	Flanking Active TSS Weak transcription Genic enhancers Strong transcription Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs324702	CDKL2	cis	cerebellum	SCAN
rs324702	FAM47E	cis	parietal	SCAN
rs324702	CDKL2	cis	parietal	SCAN
rs324702	CCNG2	cis	cerebellum	SCAN
rs324702	RCHY1	cis	cerebellum	SCAN
rs324702	FRAS1	cis	cerebellum	SCAN

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:76650800-76737800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr4:76671000-76739400	Weak transcription	Stomach Mucosa	stomach
3	chr4:76685800-76738400	Strong transcription	Monocytes-CD14+_RO01746	blood
4	chr4:76688200-76738200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
5	chr4:76707800-76738600	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr4:76720400-76738200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr4:76721400-76738200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
8	chr4:76721400-76738200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
9	chr4:76722400-76738400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr4:76724800-76738200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr4:76725000-76738000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr4:76725000-76738200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr4:76725000-76738200	Strong transcription	Primary T cells fromperipheralblood	blood
14	chr4:76725200-76738400	Strong transcription	Fetal Muscle Trunk	muscle
15	chr4:76729600-76738200	Strong transcription	HSMM	muscle
16	chr4:76730000-76738600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr4:76730000-76738800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr4:76730400-76738400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr4:76730800-76738200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr4:76731200-76737800	Weak transcription	Hela-S3	cervix
21	chr4:76731800-76738000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
22	chr4:76732600-76739400	Strong transcription	NHLF	lung
23	chr4:76732800-76738400	Strong transcription	NH-A	brain
24	chr4:76733200-76738600	Strong transcription	Muscle Satellite Cultured Cells	--
25	chr4:76734400-76738200	Strong transcription	HSMMtube	muscle
26	chr4:76735400-76738400	Strong transcription	Brain Inferior Temporal Lobe	brain
27	chr4:76735600-76738800	Strong transcription	Fetal Stomach	stomach
28	chr4:76736200-76738000	Weak transcription	Small Intestine	intestine
29	chr4:76736200-76743400	Weak transcription	Fetal Brain Male	brain
30	chr4:76736400-76738000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
31	chr4:76736400-76738000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr4:76736400-76738000	Weak transcription	Colonic Mucosa	Colon
33	chr4:76736400-76738200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr4:76736400-76738400	Weak transcription	Primary T helper cells PMA-I stimulated	--
35	chr4:76736400-76739600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr4:76736400-76739600	Weak transcription	Brain Cingulate Gyrus	brain
37	chr4:76736400-76742200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
38	chr4:76736400-76743600	Weak transcription	Colon Smooth Muscle	Colon
39	chr4:76736400-76744800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
40	chr4:76736600-76737800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr4:76736600-76737800	Weak transcription	Lung	lung
42	chr4:76736600-76738000	Weak transcription	Psoas Muscle	Psoas
43	chr4:76736600-76738200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr4:76736600-76738200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
45	chr4:76736600-76738200	Weak transcription	Thymus	Thymus
46	chr4:76736600-76738400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr4:76736600-76738800	Weak transcription	Primary T helper cells fromperipheralblood	blood
48	chr4:76736600-76739400	Weak transcription	Right Ventricle	heart
49	chr4:76736600-76739600	Weak transcription	Spleen	Spleen
50	chr4:76736600-76741200	Weak transcription	Aorta	Aorta

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