Variant report

Variant	rs4714131
Chromosome Location	chr6:38189036-38189037
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:38188305..38192389-chr6:38192840..38195857,4	K562	blood:
2	chr6:38184010..38186134-chr6:38187890..38189397,2	K562	blood:
3	chr6:38189033..38190926-chr6:38201361..38202956,2	K562	blood:

Extended variants
information (count: 34 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1931765	0.88[CEU][hapmap];0.85[MEX][hapmap];0.96[TSI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1931766	0.88[CEU][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2050161	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2395695	0.94[CEU][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2395696	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4299828	0.94[CEU][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.96[TSI][hapmap];0.87[YRI][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4711527	1.00[CEU][hapmap];0.90[GIH][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4714128	0.93[CEU][hapmap];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4714129	0.88[CEU][hapmap];0.85[MEX][hapmap];0.96[TSI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4714130	1.00[CEU][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4714132	1.00[CEU][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4714133	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6458045	0.88[CEU][hapmap]
rs6458047	1.00[CEU][hapmap];0.97[GIH][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs66634926	0.83[AMR][1000 genomes]
rs6904507	0.94[CEU][hapmap];0.87[YRI][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6915783	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6917654	1.00[CEU][hapmap];0.87[GIH][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6924088	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6930118	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6935617	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7738411	1.00[CEU][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9380722	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9380724	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9470833	0.94[CEU][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1028825	chr6:37495154-38278320	Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv1021991	chr6:37893949-38738720	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv885817	chr6:38036420-39019503	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	nsv534620	chr6:38049585-38602064	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
5	nsv522522	chr6:38131442-38207636	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases
6	nsv885818	chr6:38147745-38436317	Enhancers Weak transcription Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv885819	chr6:38148770-38190439	Flanking Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv520053	chr6:38154941-38207636	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	nsv885820	chr6:38166511-38468887	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4714131	FGD2	cis	cerebellum	SCAN
rs4714131	ZFAND3	cis	cerebellum	SCAN
rs4714131	C6orf129	cis	parietal	SCAN

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:38160800-38201400	Weak transcription	Primary B cells from peripheral blood	blood
2	chr6:38166800-38194800	Weak transcription	Primary B cells from cord blood	blood
3	chr6:38167000-38210400	Weak transcription	Primary T cells from cord blood	blood
4	chr6:38177600-38189200	Weak transcription	Gastric	stomach
5	chr6:38178000-38221600	Weak transcription	Primary T cells fromperipheralblood	blood
6	chr6:38178000-38221800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
7	chr6:38181000-38207600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr6:38181400-38191200	Weak transcription	Ovary	ovary
9	chr6:38181400-38195200	Weak transcription	Colonic Mucosa	Colon
10	chr6:38181400-38202600	Weak transcription	Fetal Stomach	stomach
11	chr6:38181400-38229400	Weak transcription	Fetal Intestine Small	intestine
12	chr6:38182200-38194000	Weak transcription	Lung	lung
13	chr6:38183200-38195200	Weak transcription	Fetal Brain Male	brain
14	chr6:38183600-38194000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr6:38184200-38197200	Weak transcription	HSMMtube	muscle
16	chr6:38184200-38202800	Weak transcription	Psoas Muscle	Psoas
17	chr6:38186600-38215200	Weak transcription	Aorta	Aorta
18	chr6:38187200-38189400	Enhancers	Brain Cingulate Gyrus	brain
19	chr6:38187400-38189200	Enhancers	Cortex derived primary cultured neurospheres	brain
20	chr6:38187400-38189200	Enhancers	Brain Angular Gyrus	brain
21	chr6:38187400-38189400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr6:38187400-38189400	Enhancers	Brain Anterior Caudate	brain
23	chr6:38187400-38189400	Enhancers	Brain Hippocampus Middle	brain
24	chr6:38187800-38189200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr6:38188000-38201200	Weak transcription	Spleen	Spleen
26	chr6:38188200-38189200	Enhancers	Brain Inferior Temporal Lobe	brain
27	chr6:38188800-38193800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr6:38189000-38189200	Enhancers	Brain Germinal Matrix	brain
29	chr6:38189000-38193600	Weak transcription	Brain Substantia Nigra	brain
30	chr6:38189000-38194000	Weak transcription	HUES6 Cell Line	embryonic stem cell
31	chr6:38189000-38194200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

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