Variant report

Variant	rs423872
Chromosome Location	chr5:52906247-52906248
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 73 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10077935	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10471875	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1465445	0.88[GIH][hapmap]
rs1532163	0.86[CHD][hapmap];0.81[GIH][hapmap]
rs1552649	0.82[ASN][1000 genomes]
rs173905	0.84[ASN][1000 genomes]
rs1844696	0.81[CHB][hapmap];0.87[ASN][1000 genomes]
rs1844698	0.87[ASN][1000 genomes]
rs187659	0.87[ASN][1000 genomes]
rs198941	0.84[ASN][1000 genomes]
rs2130744	0.85[CHB][hapmap];0.84[ASN][1000 genomes]
rs256083	0.84[ASN][1000 genomes]
rs256085	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs256087	0.85[CHB][hapmap];0.84[ASN][1000 genomes]
rs256090	0.85[CHB][hapmap];0.93[CHD][hapmap];0.86[ASN][1000 genomes]
rs256095	0.93[CHD][hapmap];0.87[ASN][1000 genomes]
rs256097	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs256107	0.93[CHD][hapmap];0.86[GIH][hapmap];0.83[ASN][1000 genomes]
rs256108	0.83[ASN][1000 genomes]
rs256110	0.82[ASN][1000 genomes]
rs256112	0.83[ASN][1000 genomes]
rs256113	0.85[ASN][1000 genomes]
rs256116	0.93[CHD][hapmap];0.87[ASN][1000 genomes]
rs256117	0.85[CHB][hapmap];0.87[ASN][1000 genomes]
rs2607501	0.87[ASN][1000 genomes]
rs2607502	0.82[ASN][1000 genomes]
rs2607509	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2607511	0.87[ASN][1000 genomes]
rs2636991	0.87[ASN][1000 genomes]
rs2636999	0.82[ASN][1000 genomes]
rs2637004	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2637027	0.87[ASN][1000 genomes]
rs2637030	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs271213	0.81[ASN][1000 genomes]
rs271214	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs271216	0.87[ASN][1000 genomes]
rs271217	0.81[ASN][1000 genomes]
rs31302	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs31303	0.85[CHB][hapmap];0.96[CHD][hapmap];0.85[GIH][hapmap];0.87[ASN][1000 genomes]
rs370594	0.87[ASN][1000 genomes]
rs372006	0.83[ASN][1000 genomes]
rs372135	0.87[ASN][1000 genomes]
rs375956	0.83[ASN][1000 genomes]
rs376566	0.87[ASN][1000 genomes]
rs381374	0.87[ASN][1000 genomes]
rs403207	0.85[CHB][hapmap];0.93[CHD][hapmap];0.86[GIH][hapmap];0.84[ASN][1000 genomes]
rs423014	0.84[CHB][hapmap];0.84[ASN][1000 genomes]
rs424955	0.90[CHD][hapmap];0.86[GIH][hapmap];0.83[ASN][1000 genomes]
rs429384	0.88[ASN][1000 genomes]
rs430427	0.87[ASN][1000 genomes]
rs435187	0.85[CHB][hapmap];0.87[ASN][1000 genomes]
rs439552	0.81[JPT][hapmap];0.85[ASN][1000 genomes]
rs439641	0.87[ASN][1000 genomes]
rs449160	0.87[ASN][1000 genomes]
rs530216	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs549131	0.84[ASN][1000 genomes]
rs6881928	0.85[ASN][1000 genomes]
rs693995	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7728496	0.85[CHB][hapmap];0.93[CHD][hapmap];0.86[GIH][hapmap];0.80[ASN][1000 genomes]
rs786333	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs786335	0.87[ASN][1000 genomes]
rs813301	0.94[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs923609	0.85[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2752745	chr5:52422063-53343529	Transcr. at gene 5' and 3' ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv1032632	chr5:52667145-53655624	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers 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 miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv880868	chr5:52799618-53002783	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv880689	chr5:52847995-53002783	ZNF genes & repeats Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv881348	chr5:52885100-52942083	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	nsv881237	chr5:52885100-52944428	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
7	nsv880426	chr5:52885100-52953048	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
8	nsv881604	chr5:52885100-53035301	Weak transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	nsv880762	chr5:52894276-52944428	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
10	nsv4828	chr5:52895470-52940279	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs423872	HEY2	trans	parietal	SCAN
rs423872	NDUFS4	cis	parietal	SCAN

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:52860000-52909000	Weak transcription	Small Intestine	intestine
2	chr5:52876800-52907400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr5:52888800-52908200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr5:52889800-52920800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr5:52890000-52912400	Weak transcription	K562	blood
6	chr5:52890200-52907200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr5:52890200-52920000	Weak transcription	HepG2	liver
8	chr5:52899200-52908400	Weak transcription	Rectal Smooth Muscle	rectum
9	chr5:52899200-52908400	Weak transcription	HMEC	breast
10	chr5:52899200-52910200	Weak transcription	Brain Germinal Matrix	brain
11	chr5:52899400-52908200	Weak transcription	Colon Smooth Muscle	Colon
12	chr5:52899400-52908200	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr5:52899400-52908400	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr5:52899400-52908400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr5:52899400-52928400	Weak transcription	Fetal Heart	heart
16	chr5:52899800-52906400	Strong transcription	Primary monocytes fromperipheralblood	blood
17	chr5:52900800-52908600	Weak transcription	A549	lung
18	chr5:52900800-52909000	Weak transcription	Esophagus	oesophagus
19	chr5:52900800-52910200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
20	chr5:52900800-52911800	Weak transcription	Brain Substantia Nigra	brain
21	chr5:52900800-52936600	Weak transcription	NHEK	skin
22	chr5:52901000-52932600	Weak transcription	Aorta	Aorta
23	chr5:52901400-52920600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
24	chr5:52901600-52907200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
25	chr5:52901600-52918000	Weak transcription	Primary T helper cells PMA-I stimulated	--
26	chr5:52901600-52919600	Weak transcription	Primary T helper cells fromperipheralblood	blood
27	chr5:52901800-52927000	Weak transcription	Pancreas	Pancrea
28	chr5:52902200-52906600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
29	chr5:52902400-52907800	Weak transcription	Fetal Thymus	thymus
30	chr5:52902600-52907000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr5:52902600-52907400	Weak transcription	Fetal Stomach	stomach
32	chr5:52902600-52909000	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr5:52902600-52919600	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr5:52902600-52920800	Weak transcription	Fetal Intestine Small	intestine
35	chr5:52902600-52927000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr5:52902800-52907200	Weak transcription	HUES6 Cell Line	embryonic stem cell
37	chr5:52902800-52908400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr5:52902800-52918800	Weak transcription	Rectal Mucosa Donor 31	rectum
39	chr5:52902800-52920800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr5:52902800-52926400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr5:52903000-52908400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr5:52903000-52927000	Weak transcription	Left Ventricle	heart
43	chr5:52903000-52943800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
44	chr5:52903200-52907200	Weak transcription	Fetal Intestine Large	intestine
45	chr5:52903200-52909200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
46	chr5:52903200-52910400	Weak transcription	Brain Hippocampus Middle	brain
47	chr5:52903200-52918200	Weak transcription	Liver	Liver
48	chr5:52903200-52918400	Weak transcription	Primary B cells from cord blood	blood
49	chr5:52903200-52918800	Weak transcription	Duodenum Mucosa	Duodenum
50	chr5:52903200-52919800	Weak transcription	Fetal Muscle Leg	muscle

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