Variant report

Variant	rs6544221
Chromosome Location	chr2:39600722-39600723
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 55 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10175094	0.91[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10185961	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs10193807	0.88[ASN][1000 genomes]
rs10196407	0.84[CHB][hapmap]
rs10865148	0.92[CHB][hapmap];0.90[CHD][hapmap];0.88[JPT][hapmap]
rs11124671	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs11124675	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs11124680	0.92[CHB][hapmap];0.93[JPT][hapmap]
rs11677383	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs11677611	0.82[ASN][1000 genomes]
rs12151392	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs12328727	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12617901	0.82[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.88[GIH][hapmap];0.95[TSI][hapmap];0.90[EUR][1000 genomes]
rs12624242	0.90[CHD][hapmap]
rs12712634	1.00[CHB][hapmap];0.93[CHD][hapmap];0.88[JPT][hapmap]
rs12712636	0.81[AMR][1000 genomes]
rs12712640	1.00[CHB][hapmap];0.90[CHD][hapmap];0.88[JPT][hapmap];0.81[MEX][hapmap]
rs12712642	0.82[ASN][1000 genomes]
rs13425432	0.82[JPT][hapmap]
rs1558854	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1861733	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs1861734	1.00[CHB][hapmap];0.90[CHD][hapmap];0.94[JPT][hapmap]
rs2024514	1.00[CHB][hapmap];0.93[CHD][hapmap];0.88[JPT][hapmap];0.81[MEX][hapmap]
rs3755171	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs3755176	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs3770662	0.86[CHB][hapmap];0.88[JPT][hapmap]
rs3770664	1.00[CHB][hapmap];0.86[CHD][hapmap];0.88[JPT][hapmap];0.81[MEX][hapmap]
rs3770671	1.00[CHB][hapmap];0.90[CHD][hapmap];0.94[JPT][hapmap];0.82[MEX][hapmap];0.81[TSI][hapmap]
rs3770672	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs3887311	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6544214	1.00[CHB][hapmap];0.83[CHD][hapmap]
rs6709424	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs6714566	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs6721049	1.00[ASW][hapmap]
rs6743345	0.84[CHB][hapmap]
rs7340455	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs7421175	0.81[ASN][1000 genomes]
rs7561630	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7573923	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs7598583	0.82[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs7603337	0.88[ASN][1000 genomes]
rs9037	1.00[CHB][hapmap];0.83[CHD][hapmap];0.94[JPT][hapmap];0.81[TSI][hapmap]
rs9309036	0.86[MEX][hapmap]
rs9309037	0.88[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010874	chr2:39255376-39604535	Strong transcription Flanking Active TSS Enhancers Active TSS Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
2	nsv535649	chr2:39255376-39604535	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
3	nsv531346	chr2:39263225-39606367	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
4	nsv1009379	chr2:39271472-39604535	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
5	nsv581494	chr2:39277851-39626388	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
6	esv1827292	chr2:39385155-39675339	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
7	esv1812828	chr2:39396457-39675339	Flanking Active TSS Strong transcription Active TSS Enhancers Weak transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
8	nsv833847	chr2:39410762-39604640	ZNF genes & repeats Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
9	nsv533445	chr2:39412970-39605266	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
10	nsv873887	chr2:39468676-39601889	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
11	nsv997934	chr2:39473548-39751029	Enhancers Strong transcription ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6544221	CDKL4	cis	brain	BrainEAC

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39584400-39604600	Weak transcription	Right Ventricle	heart
2	chr2:39587000-39608800	Weak transcription	Pancreas	Pancrea
3	chr2:39587200-39604400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr2:39587800-39604800	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr2:39588000-39607800	Weak transcription	Ovary	ovary
6	chr2:39588000-39608800	Weak transcription	Lung	lung
7	chr2:39588000-39609000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr2:39588000-39630400	Weak transcription	Placenta	Placenta
9	chr2:39588200-39602800	Weak transcription	Duodenum Mucosa	Duodenum
10	chr2:39588200-39603000	Weak transcription	Adipose Nuclei	Adipose
11	chr2:39588400-39603000	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr2:39590000-39604800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr2:39590200-39602800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr2:39590200-39602800	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr2:39590200-39604800	Weak transcription	HSMMtube	muscle
16	chr2:39590400-39602400	Weak transcription	Liver	Liver
17	chr2:39590600-39601000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr2:39590600-39601200	Weak transcription	Fetal Stomach	stomach
19	chr2:39590600-39602200	Weak transcription	Fetal Muscle Trunk	muscle
20	chr2:39591000-39602000	Weak transcription	Fetal Thymus	thymus
21	chr2:39591800-39602200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr2:39591800-39604600	Weak transcription	NH-A	brain
23	chr2:39591800-39621400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr2:39592000-39606800	Weak transcription	Stomach Smooth Muscle	stomach
25	chr2:39592400-39604600	Weak transcription	Fetal Heart	heart
26	chr2:39592600-39607000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
27	chr2:39592800-39617600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr2:39593400-39603200	Weak transcription	K562	blood
29	chr2:39593800-39602800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr2:39594000-39600800	Weak transcription	Fetal Intestine Small	intestine
31	chr2:39594600-39608800	Weak transcription	Left Ventricle	heart
32	chr2:39595800-39604600	Weak transcription	Psoas Muscle	Psoas
33	chr2:39595800-39606800	Weak transcription	HUVEC	blood vessel
34	chr2:39595800-39607200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr2:39596200-39602400	Weak transcription	Primary T helper cells PMA-I stimulated	--
36	chr2:39596200-39605000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
37	chr2:39596400-39604600	Weak transcription	Skeletal Muscle Male	skeletal muscle
38	chr2:39596400-39605000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
39	chr2:39596400-39606800	Weak transcription	Fetal Brain Male	brain
40	chr2:39596600-39602400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr2:39596800-39604000	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr2:39596800-39605600	Weak transcription	Primary T helper cells fromperipheralblood	blood
43	chr2:39597200-39607800	Weak transcription	Small Intestine	intestine
44	chr2:39597600-39600800	Weak transcription	NHEK	skin
45	chr2:39597600-39602800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr2:39597600-39603000	Weak transcription	NHLF	lung
47	chr2:39597600-39604400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
48	chr2:39597600-39604800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
49	chr2:39597600-39605600	Weak transcription	Brain Hippocampus Middle	brain
50	chr2:39597600-39606200	Weak transcription	Brain Anterior Caudate	brain

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