Variant report

Variant	rs324740
Chromosome Location	chr4:76715678-76715679
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:76707581..76709648-chr4:76714375..76715903,2	K562	blood:
2	chr4:76715216..76717144-chr4:76717984..76719951,2	K562	blood:
3	chr4:76647935..76649552-chr4:76714127..76716514,2	K562	blood:

Extended variants
information (count: 88 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs10028291	0.93[ASW][hapmap];0.91[LWK][hapmap];0.84[YRI][hapmap]
rs10031352	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10212995	0.86[ASW][hapmap]
rs10856853	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs11097112	0.84[YRI][hapmap];0.88[AFR][1000 genomes]
rs11097117	0.94[ASN][1000 genomes]
rs11097121	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs11097122	0.91[AFR][1000 genomes]
rs11556146	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs11727895	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11728073	0.91[AFR][1000 genomes]
rs11732850	0.80[ASN][1000 genomes]
rs11734358	0.87[ASN][1000 genomes]
rs11935073	0.85[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs12233780	0.94[ASN][1000 genomes]
rs12498415	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs12505147	0.92[ASN][1000 genomes]
rs12505149	0.88[AFR][1000 genomes]
rs12506101	0.92[ASN][1000 genomes]
rs12508200	0.84[ASN][1000 genomes]
rs12508992	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12511212	0.94[ASN][1000 genomes]
rs12511575	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs13133144	0.84[YRI][hapmap];0.81[AFR][1000 genomes]
rs13137229	0.80[ASN][1000 genomes]
rs13145290	0.93[ASW][hapmap];0.93[LWK][hapmap];0.84[YRI][hapmap];0.91[AFR][1000 genomes]
rs16996019	0.91[CEU][hapmap];0.85[CHB][hapmap];0.88[CHD][hapmap];0.91[GIH][hapmap];0.92[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.96[YRI][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17000786	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17000794	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs17000864	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs186563	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2089253	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2175640	0.84[ASN][1000 genomes]
rs2271472	0.84[YRI][hapmap];0.91[AFR][1000 genomes]
rs28573275	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28680723	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2869175	0.83[AFR][1000 genomes]
rs324686	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs324688	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs324690	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.92[JPT][hapmap];1.00[LWK][hapmap];0.89[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs324691	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs324693	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs324694	0.87[TSI][hapmap]
rs324696	0.95[CEU][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs324697	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs324698	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs324700	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs324701	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs324703	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs324709	1.00[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs324712	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs324713	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs324714	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs324719	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs324722	0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs324723	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs324726	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap]
rs324727	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs324730	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs324731	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs324733	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs324734	0.87[TSI][hapmap]
rs324735	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs324738	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34855591	0.81[ASN][1000 genomes]
rs4262008	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4859408	0.93[ASW][hapmap];0.93[LWK][hapmap];0.84[YRI][hapmap];0.83[AFR][1000 genomes]
rs4859409	0.90[AFR][1000 genomes]
rs4859555	0.88[AFR][1000 genomes]
rs61603278	0.94[ASN][1000 genomes]
rs6531816	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs6531901	0.84[YRI][hapmap];0.81[AFR][1000 genomes]
rs6531934	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs6822619	0.89[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs6827016	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6847333	0.93[ASW][hapmap];0.89[LWK][hapmap]
rs6856162	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs72858061	0.94[ASN][1000 genomes]
rs7340822	0.85[CHB][hapmap]
rs7657198	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7663617	0.91[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7680729	0.91[ASN][1000 genomes]
rs7684778	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7693127	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs324740	FAM47E	cis	parietal	SCAN
rs324740	DLK2	trans	cerebellum	SCAN
rs324740	CDKL2	cis	parietal	SCAN

Chromatin state (count:124 , 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	chr4:76675000-76727400	Strong transcription	HUES64 Cell Line	embryonic stem cell
5	chr4:76676400-76730600	Weak transcription	Spleen	Spleen
6	chr4:76677000-76736200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr4:76685800-76719200	Strong transcription	Primary monocytes fromperipheralblood	blood
8	chr4:76685800-76738400	Strong transcription	Monocytes-CD14+_RO01746	blood
9	chr4:76687600-76716200	Strong transcription	HUES6 Cell Line	embryonic stem cell
10	chr4:76688200-76738200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
11	chr4:76689400-76724000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr4:76691200-76717000	Strong transcription	Placenta	Placenta
13	chr4:76691800-76716800	Strong transcription	Fetal Intestine Large	intestine
14	chr4:76692000-76717400	Strong transcription	Rectal Mucosa Donor 29	rectum
15	chr4:76695000-76717200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr4:76697600-76734400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr4:76698000-76721600	Weak transcription	Brain Anterior Caudate	brain
18	chr4:76698000-76735400	Weak transcription	Small Intestine	intestine
19	chr4:76698800-76725000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr4:76699000-76725400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr4:76699200-76717400	Strong transcription	Liver	Liver
22	chr4:76699200-76724000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr4:76699400-76722600	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr4:76701200-76725200	Weak transcription	Thymus	Thymus
25	chr4:76701800-76721800	Weak transcription	Colonic Mucosa	Colon
26	chr4:76703400-76722800	Weak transcription	Psoas Muscle	Psoas
27	chr4:76704200-76722400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
28	chr4:76704800-76725200	Weak transcription	Brain Cingulate Gyrus	brain
29	chr4:76705000-76730800	Weak transcription	Fetal Heart	heart
30	chr4:76705800-76721400	Weak transcription	Colon Smooth Muscle	Colon
31	chr4:76705800-76725200	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr4:76705800-76730600	Weak transcription	Fetal Brain Female	brain
33	chr4:76706000-76722800	Weak transcription	Ovary	ovary
34	chr4:76706000-76730600	Weak transcription	Aorta	Aorta
35	chr4:76706000-76732000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr4:76706000-76732000	Weak transcription	Gastric	stomach
37	chr4:76706200-76725000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr4:76707200-76715800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr4:76707600-76718400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr4:76707800-76716400	Strong transcription	Osteobl	bone
41	chr4:76707800-76738600	Weak transcription	Pancreatic Islets	Pancreatic Islet
42	chr4:76708000-76715800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr4:76708000-76716400	Strong transcription	H1 Cell Line	embryonic stem cell
44	chr4:76708000-76716800	Strong transcription	Primary T helper cells PMA-I stimulated	--
45	chr4:76708000-76717400	Strong transcription	Duodenum Mucosa	Duodenum
46	chr4:76708400-76721400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
47	chr4:76708400-76725200	Weak transcription	Brain Hippocampus Middle	brain
48	chr4:76708400-76735400	Weak transcription	Right Ventricle	heart
49	chr4:76709000-76716000	Strong transcription	Fetal Lung	lung
50	chr4:76710000-76716400	Strong transcription	NH-A	brain

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