Variant report

Variant	rs324734
Chromosome Location	chr4:76706696-76706697
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:76704931..76708571-chr4:76709075..76713501,5	K562	blood:
2	chr4:76705586..76707502-chr4:76725352..76727838,2	K562	blood:
3	chr4:76683893..76685556-chr4:76704376..76707290,2	K562	blood:
4	chr4:76683893..76686994-chr4:76703855..76707290,3	K562	blood:

Variant related genes	Relation type
ENSG00000138768	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10031532	1.00[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17000786	0.87[TSI][hapmap]
rs28541901	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs324687	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs324690	0.87[TSI][hapmap]
rs324694	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];0.80[YRI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs324702	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs324704	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs324705	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs324706	0.84[ASW][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[MKK][hapmap];0.85[TSI][hapmap];0.87[YRI][hapmap];0.87[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs324710	1.00[CEU][hapmap];0.95[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs324720	0.84[CEU][hapmap];0.92[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs324726	0.87[TSI][hapmap]
rs324727	0.87[TSI][hapmap]
rs324729	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs324735	0.87[TSI][hapmap]
rs324736	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs324739	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs324740	0.87[TSI][hapmap]
rs41398350	1.00[CHD][hapmap]
rs4262008	0.83[TSI][hapmap]
rs55884734	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6817228	0.84[EUR][1000 genomes]
rs6823013	1.00[CHD][hapmap]
rs6841486	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7691515	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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	nsv1003516	chr4:76597112-76729576	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
3	nsv537143	chr4:76597112-76729576	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
4	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
rs324734	CDKL2	cis	cerebellum	SCAN
rs324734	CCNG2	cis	cerebellum	SCAN
rs324734	FRAS1	cis	cerebellum	SCAN
rs324734	CDKL2	cis	parietal	SCAN
rs324734	RCHY1	cis	cerebellum	SCAN
rs324734	FAM47E	cis	parietal	SCAN

Chromatin state (count:126 , 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	chr4:76652400-76725000	Weak transcription	Hela-S3	cervix
3	chr4:76671000-76739400	Weak transcription	Stomach Mucosa	stomach
4	chr4:76671600-76707800	Weak transcription	Right Ventricle	heart
5	chr4:76674800-76715200	Strong transcription	HUES48 Cell Line	embryonic stem cell
6	chr4:76675000-76727400	Strong transcription	HUES64 Cell Line	embryonic stem cell
7	chr4:76676400-76730600	Weak transcription	Spleen	Spleen
8	chr4:76677000-76710200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr4:76677000-76736200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr4:76685800-76719200	Strong transcription	Primary monocytes fromperipheralblood	blood
11	chr4:76685800-76738400	Strong transcription	Monocytes-CD14+_RO01746	blood
12	chr4:76687600-76716200	Strong transcription	HUES6 Cell Line	embryonic stem cell
13	chr4:76688200-76738200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
14	chr4:76689400-76724000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr4:76689800-76709200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
16	chr4:76691200-76713600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr4:76691200-76717000	Strong transcription	Placenta	Placenta
18	chr4:76691400-76715400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr4:76691600-76707200	Strong transcription	Duodenum Mucosa	Duodenum
20	chr4:76691600-76710000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr4:76691600-76710400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr4:76691800-76708600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
23	chr4:76691800-76716800	Strong transcription	Fetal Intestine Large	intestine
24	chr4:76692000-76709800	Strong transcription	Fetal Thymus	thymus
25	chr4:76692000-76717400	Strong transcription	Rectal Mucosa Donor 29	rectum
26	chr4:76692400-76708600	Strong transcription	Duodenum Smooth Muscle	Duodenum
27	chr4:76695000-76708400	Strong transcription	HSMM	muscle
28	chr4:76695000-76717200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr4:76695200-76709200	Strong transcription	Skeletal Muscle Female	skeletal muscle
30	chr4:76697600-76734400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
31	chr4:76698000-76711400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
32	chr4:76698000-76711600	Weak transcription	Brain Angular Gyrus	brain
33	chr4:76698000-76721600	Weak transcription	Brain Anterior Caudate	brain
34	chr4:76698000-76735400	Weak transcription	Small Intestine	intestine
35	chr4:76698600-76711400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
36	chr4:76698800-76725000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr4:76699000-76725400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr4:76699200-76707600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
39	chr4:76699200-76710400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr4:76699200-76717400	Strong transcription	Liver	Liver
41	chr4:76699200-76724000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr4:76699400-76707600	Weak transcription	Pancreatic Islets	Pancreatic Islet
43	chr4:76699400-76711400	Weak transcription	Brain Substantia Nigra	brain
44	chr4:76699400-76722600	Weak transcription	Placenta Amnion	Placenta Amnion
45	chr4:76701200-76708600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr4:76701200-76711400	Weak transcription	Fetal Kidney	kidney
47	chr4:76701200-76712000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr4:76701200-76725200	Weak transcription	Thymus	Thymus
49	chr4:76701400-76711200	Weak transcription	K562	blood
50	chr4:76701800-76721800	Weak transcription	Colonic Mucosa	Colon

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