Variant report

Variant	rs6831643
Chromosome Location	chr4:99476287-99476288
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 46 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10002696	0.92[CEU][hapmap]
rs10006366	0.92[CEU][hapmap]
rs10018825	0.88[CEU][hapmap];0.94[JPT][hapmap]
rs10021296	0.88[CEU][hapmap];0.94[JPT][hapmap]
rs10025051	0.92[CEU][hapmap]
rs11097621	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11730384	1.00[JPT][hapmap]
rs13108940	0.92[CEU][hapmap]
rs13114571	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13132635	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13134231	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs13137132	0.81[CEU][hapmap]
rs13141997	0.92[CEU][hapmap];0.88[EUR][1000 genomes]
rs13149070	0.88[CEU][hapmap];0.94[JPT][hapmap]
rs1534555	0.92[CEU][hapmap]
rs1573478	0.92[CEU][hapmap]
rs17191936	0.80[CHB][hapmap]
rs17192060	0.83[CHB][hapmap]
rs1919211	0.80[CEU][hapmap];0.94[JPT][hapmap];0.80[MEX][hapmap]
rs2037832	0.92[CEU][hapmap]
rs2866017	0.87[CEU][hapmap];0.94[JPT][hapmap]
rs4699343	0.92[CEU][hapmap]
rs4699346	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4699348	0.91[CEU][hapmap]
rs4699349	0.96[CEU][hapmap];0.81[EUR][1000 genomes]
rs4699639	0.92[CEU][hapmap]
rs4699640	0.92[CEU][hapmap]
rs4699644	0.92[CEU][hapmap]
rs4699650	0.94[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.84[TSI][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4699651	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4699652	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6532742	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6532744	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6532745	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6532747	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6532748	0.81[CHD][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap]
rs6827510	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6831464	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6837359	0.96[CEU][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6846287	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6854339	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7672134	0.88[CEU][hapmap];0.94[JPT][hapmap]
rs7695093	0.83[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2754250	chr4:99094922-99527122	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers 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	20 gene(s)	inside rSNPs	diseases
2	nsv1004181	chr4:99208152-99529576	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	esv2760882	chr4:99460485-99521345	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6831643	H2AFZ	cis	parietal	SCAN
rs6831643	TSPAN5	cis	cerebellum	SCAN

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:99459200-99479600	Weak transcription	Spleen	Spleen
2	chr4:99463800-99478800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr4:99466400-99477000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr4:99466600-99479800	Weak transcription	Fetal Thymus	thymus
5	chr4:99466800-99501600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr4:99468400-99482200	Weak transcription	Esophagus	oesophagus
7	chr4:99468600-99477000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr4:99468600-99477000	Weak transcription	HMEC	breast
9	chr4:99468800-99477000	Weak transcription	HSMMtube	muscle
10	chr4:99468800-99477200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr4:99469000-99476600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr4:99469000-99482800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr4:99474000-99477400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr4:99474000-99477400	Weak transcription	HSMM	muscle
15	chr4:99475200-99482400	Enhancers	Cortex derived primary cultured neurospheres	brain
16	chr4:99475400-99478200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr4:99475400-99481400	Enhancers	Brain Hippocampus Middle	brain
18	chr4:99475400-99482000	Enhancers	Brain Cingulate Gyrus	brain
19	chr4:99475400-99482200	Enhancers	Brain Angular Gyrus	brain
20	chr4:99475600-99480600	Enhancers	Brain Germinal Matrix	brain
21	chr4:99475600-99481400	Enhancers	Brain Substantia Nigra	brain
22	chr4:99475800-99479200	Enhancers	iPS-20b Cell Line	embryonic stem cell
23	chr4:99475800-99479400	Enhancers	iPS-18 Cell Line	embryonic stem cell
24	chr4:99475800-99482200	Enhancers	Brain Inferior Temporal Lobe	brain
25	chr4:99476000-99477200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
26	chr4:99476000-99477400	Enhancers	Fetal Brain Male	brain
27	chr4:99476000-99477600	Enhancers	iPS-15b Cell Line	embryonic stem cell
28	chr4:99476000-99477600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
29	chr4:99476000-99477800	Enhancers	H1 Cell Line	embryonic stem cell
30	chr4:99476000-99477800	Enhancers	Brain Anterior Caudate	brain
31	chr4:99476000-99479000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
32	chr4:99476000-99479200	Enhancers	Muscle Satellite Cultured Cells	--
33	chr4:99476000-99479200	Enhancers	HUVEC	blood vessel
34	chr4:99476000-99479400	Enhancers	ES-I3 Cell Line	embryonic stem cell
35	chr4:99476000-99479600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr4:99476000-99479800	Enhancers	HUES6 Cell Line	embryonic stem cell
37	chr4:99476000-99481200	Enhancers	HUES64 Cell Line	embryonic stem cell
38	chr4:99476000-99482200	Enhancers	Fetal Brain Female	brain
39	chr4:99476200-99476400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr4:99476200-99476400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr4:99476200-99476400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr4:99476200-99476400	Enhancers	NH-A	brain
43	chr4:99476200-99476800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr4:99476200-99477400	Enhancers	H9 Cell Line	embryonic stem cell
45	chr4:99476200-99477400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr4:99476200-99477400	Enhancers	Fetal Heart	heart
47	chr4:99476200-99477800	Enhancers	Ovary	ovary
48	chr4:99476200-99478000	Enhancers	Breast Myoepithelial Primary Cells	Breast
49	chr4:99476200-99479200	Enhancers	Osteobl	bone

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