Variant report

Variant	rs10002498
Chromosome Location	chr4:47928585-47928586
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:47928329..47929479-chr4:48088621..48089783,3	K562	blood:
2	chr4:47914012..47917930-chr4:47928517..47931716,3	K562	blood:
3	chr4:47928537..47929256-chr4:48142747..48143293,3	K562	blood:

Variant related genes	Relation type
ENSG00000170448	Chromatin interaction
ENSG00000163293	Chromatin interaction

Extended variants
information (count: 109 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:106)

rs_ID	r²[population]
rs10020447	0.94[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10025104	0.97[GIH][hapmap];0.82[TSI][hapmap]
rs1036681	0.94[CEU][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10461075	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10805158	0.84[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs10938498	0.81[EUR][1000 genomes]
rs10938508	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11732840	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11946535	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12506026	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12647189	0.94[CEU][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13143926	0.87[ASN][1000 genomes]
rs1348023	0.83[CEU][hapmap];0.93[GIH][hapmap];0.96[TSI][hapmap]
rs1371728	1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1440220	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs1440222	1.00[ASN][1000 genomes]
rs1507922	0.90[GIH][hapmap];0.85[TSI][hapmap]
rs1545200	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1550444	0.94[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs167692	0.83[CEU][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap]
rs1808853	0.88[EUR][1000 genomes]
rs1812964	0.89[CEU][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs188900	1.00[ASN][1000 genomes]
rs1968542	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1972883	0.94[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1972884	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2014934	0.94[CEU][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2033894	0.93[EUR][1000 genomes]
rs2033895	0.92[ASW][hapmap];0.94[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.97[TSI][hapmap];0.84[AFR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2053404	0.97[GIH][hapmap];0.82[TSI][hapmap]
rs2119204	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2119205	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2119207	0.94[CEU][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2119208	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs224801	0.87[ASN][1000 genomes]
rs2289433	0.97[GIH][hapmap]
rs2352456	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2352457	1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2352463	0.94[CEU][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2352466	0.94[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2581496	1.00[ASN][1000 genomes]
rs28464733	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2882950	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3113877	1.00[ASN][1000 genomes]
rs3113879	1.00[ASN][1000 genomes]
rs3113880	0.87[ASN][1000 genomes]
rs321625	1.00[ASN][1000 genomes]
rs321639	0.89[ASN][1000 genomes]
rs321640	1.00[ASN][1000 genomes]
rs321641	0.87[ASN][1000 genomes]
rs321647	0.87[ASN][1000 genomes]
rs321649	0.87[ASN][1000 genomes]
rs3762858	0.94[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3762859	0.94[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3811761	0.94[CEU][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3845160	0.94[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4308343	0.94[CEU][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4365692	0.94[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4507330	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4694868	0.94[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4694871	0.92[ASW][hapmap];0.94[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.97[TSI][hapmap];0.84[AFR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4694872	0.97[GIH][hapmap];0.82[TSI][hapmap]
rs4694875	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4694878	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4695287	0.94[CEU][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4695294	0.82[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs4695296	0.94[CEU][hapmap];0.93[EUR][1000 genomes]
rs4695302	0.94[CEU][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4695303	0.97[GIH][hapmap];0.82[TSI][hapmap]
rs4695306	0.97[GIH][hapmap];0.82[TSI][hapmap]
rs4695309	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4695312	0.94[CEU][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4695316	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6414687	0.97[GIH][hapmap];0.82[TSI][hapmap]
rs6447593	0.80[CEU][hapmap]
rs6447596	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6447599	0.94[CEU][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6447602	0.84[EUR][1000 genomes]
rs6815975	0.94[CEU][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6818556	0.97[GIH][hapmap];0.82[TSI][hapmap]
rs6819506	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6823572	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6826190	0.94[CEU][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6826909	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6827508	0.88[CEU][hapmap]
rs6829073	0.92[ASW][hapmap];0.94[CEU][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap]
rs6832334	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6833320	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6841271	0.83[CEU][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap]
rs6845451	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6850142	0.94[CEU][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs707723	0.94[CEU][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7668778	0.94[CEU][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7670219	0.94[CEU][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7671780	1.00[JPT][hapmap]
rs7672090	0.94[CEU][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7690406	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7690522	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs893861	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs893863	0.94[CEU][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs893864	0.94[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs920463	0.94[CEU][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9291317	0.97[GIH][hapmap];0.82[TSI][hapmap]
rs9291318	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9291319	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9995022	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	esv3447039	chr4:47822266-48285222	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
2	nsv1013947	chr4:47915527-48052824	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv537082	chr4:47915527-48052824	Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10002498	CNGA1	cis	Heart Left Ventricle	GTEx
rs10002498	CNGA1	cis	Thyroid	GTEx
rs10002498	NFXL1	cis	multi-tissue	Pritchard

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:47924800-47928600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
2	chr4:47924800-47928800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr4:47924800-47928800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr4:47924800-47928800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr4:47925000-47928600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr4:47925000-47928600	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr4:47925000-47928800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr4:47925000-47928800	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr4:47925000-47928800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr4:47925000-47928800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr4:47925000-47928800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr4:47925000-47928800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr4:47925200-47928600	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr4:47925200-47928800	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr4:47926000-47928600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr4:47926000-47928800	Weak transcription	GM12878-XiMat	blood
17	chr4:47926200-47928800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
18	chr4:47926400-47928600	Weak transcription	Primary neutrophils fromperipheralblood	blood
19	chr4:47928200-47928800	Enhancers	Fetal Intestine Large	intestine
20	chr4:47928200-47929200	Enhancers	Placenta Amnion	Placenta Amnion
21	chr4:47928400-47928600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr4:47928400-47928600	Enhancers	Brain Inferior Temporal Lobe	brain
23	chr4:47928400-47928600	Enhancers	Fetal Lung	lung
24	chr4:47928400-47928600	Enhancers	Monocytes-CD14+_RO01746	blood
25	chr4:47928400-47928800	Active TSS	Brain Cingulate Gyrus	brain
26	chr4:47928400-47928800	Enhancers	NHEK	skin
27	chr4:47928400-47929000	Active TSS	Duodenum Smooth Muscle	Duodenum
28	chr4:47928400-47929200	Enhancers	Breast Myoepithelial Primary Cells	Breast

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