Variant report

Variant	rs242287
Chromosome Location	chr6:88071825-88071826
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:88069946..88072865-chr6:88409522..88411370,2	K562	blood:

Variant related genes	Relation type
ENSG00000135334	Chromatin interaction

Extended variants
information (count: 143 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:141)

rs_ID	r²[population]
rs107689	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs107690	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1080595	0.82[EUR][1000 genomes]
rs1080596	0.85[CEU][hapmap];0.81[CHB][hapmap];0.91[JPT][hapmap];0.82[EUR][1000 genomes]
rs1201409	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12190280	0.91[EUR][1000 genomes]
rs12207825	0.88[EUR][1000 genomes]
rs12664578	0.82[EUR][1000 genomes]
rs173333	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1753153	0.96[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.91[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap]
rs1753154	0.96[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs183599	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.88[YRI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1925695	0.85[CEU][hapmap];0.85[CHB][hapmap];0.98[CHD][hapmap];0.90[JPT][hapmap];0.85[MEX][hapmap];0.98[TSI][hapmap];0.82[EUR][1000 genomes]
rs1980790	0.85[CEU][hapmap];0.81[CHB][hapmap];0.91[JPT][hapmap];0.82[EUR][1000 genomes]
rs1980792	0.80[CHB][hapmap];0.94[JPT][hapmap];0.82[EUR][1000 genomes]
rs2025630	0.82[EUR][1000 genomes]
rs2031518	0.81[EUR][1000 genomes]
rs2147917	0.81[CHB][hapmap];0.91[JPT][hapmap]
rs2147918	0.86[CHB][hapmap];0.91[JPT][hapmap]
rs2147919	0.81[EUR][1000 genomes]
rs2147920	0.85[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap];0.82[EUR][1000 genomes]
rs2147921	0.85[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.82[EUR][1000 genomes]
rs2182181	0.81[EUR][1000 genomes]
rs2207144	0.90[MEX][hapmap]
rs2240459	0.88[EUR][1000 genomes]
rs242267	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs242270	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs242278	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs242279	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs242280	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs242281	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs242283	0.96[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs242285	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs242286	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2474349	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2985039	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs369674	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3734187	0.86[CHB][hapmap];0.98[CHD][hapmap];0.91[JPT][hapmap]
rs373646	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs376633	0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3812130	0.85[CHB][hapmap];0.98[CHD][hapmap];0.91[JPT][hapmap]
rs3812132	0.85[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap];0.87[EUR][1000 genomes]
rs381782	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3846776	0.86[CHB][hapmap];0.98[CHD][hapmap];0.91[JPT][hapmap]
rs3857483	0.86[CHB][hapmap];0.91[JPT][hapmap]
rs3857484	0.86[CHB][hapmap];0.87[JPT][hapmap]
rs3857485	0.86[EUR][1000 genomes]
rs3857488	0.85[CEU][hapmap];0.86[CHB][hapmap];0.98[CHD][hapmap];0.91[JPT][hapmap];0.93[TSI][hapmap];0.89[EUR][1000 genomes]
rs390272	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3903920	0.85[CEU][hapmap];0.86[CHB][hapmap];0.98[CHD][hapmap];0.91[JPT][hapmap];0.85[MEX][hapmap];0.98[TSI][hapmap];0.83[EUR][1000 genomes]
rs3904088	0.85[CEU][hapmap];0.81[CHB][hapmap];0.91[JPT][hapmap];0.83[EUR][1000 genomes]
rs395358	0.82[AFR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4099964	0.86[CHB][hapmap];0.91[JPT][hapmap]
rs4110984	0.85[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap];0.83[EUR][1000 genomes]
rs4110985	0.83[EUR][1000 genomes]
rs445434	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs446851	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs447077	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs448580	0.96[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.91[JPT][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs451089	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs451465	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs451829	0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4605853	0.85[CEU][hapmap];0.86[CHB][hapmap];0.87[JPT][hapmap];0.82[EUR][1000 genomes]
rs4706289	0.85[CEU][hapmap];0.81[CHB][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap];0.85[MEX][hapmap];0.98[TSI][hapmap];0.82[EUR][1000 genomes]
rs4707346	0.85[CEU][hapmap];0.86[CHB][hapmap];0.98[CHD][hapmap];0.91[JPT][hapmap];0.85[MEX][hapmap];0.98[TSI][hapmap];0.82[EUR][1000 genomes]
rs4707347	0.82[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap];0.83[EUR][1000 genomes]
rs4707348	0.86[CHB][hapmap];0.87[JPT][hapmap]
rs4707351	0.85[CEU][hapmap];0.86[CHB][hapmap];0.98[CHD][hapmap];0.91[JPT][hapmap];0.85[MEX][hapmap];0.95[TSI][hapmap];0.82[EUR][1000 genomes]
rs4707352	0.82[EUR][1000 genomes]
rs4707356	0.87[EUR][1000 genomes]
rs4707358	0.85[CEU][hapmap];0.86[CHB][hapmap];0.98[CHD][hapmap];0.91[JPT][hapmap];0.98[TSI][hapmap];0.88[EUR][1000 genomes]
rs499373	0.83[EUR][1000 genomes]
rs586771	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59322	0.89[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap]
rs6454591	0.85[CEU][hapmap];0.81[CHB][hapmap];0.91[JPT][hapmap];0.82[EUR][1000 genomes]
rs6454592	0.82[EUR][1000 genomes]
rs6454593	0.84[CHB][hapmap];0.90[JPT][hapmap]
rs6454594	0.82[EUR][1000 genomes]
rs6454595	0.86[EUR][1000 genomes]
rs6454598	0.88[EUR][1000 genomes]
rs6454600	0.89[EUR][1000 genomes]
rs6903219	0.96[CEU][hapmap];0.95[CHB][hapmap];0.88[EUR][1000 genomes]
rs6904310	0.85[CEU][hapmap];0.81[CHB][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap];0.85[MEX][hapmap];0.98[TSI][hapmap];0.82[EUR][1000 genomes]
rs6909021	0.85[CEU][hapmap];0.81[CHB][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap];0.85[MEX][hapmap];0.98[TSI][hapmap];0.82[EUR][1000 genomes]
rs6909200	0.85[CEU][hapmap];0.81[CHB][hapmap];0.91[JPT][hapmap];0.80[MEX][hapmap];0.95[TSI][hapmap];0.82[EUR][1000 genomes]
rs6913721	0.82[EUR][1000 genomes]
rs6913932	0.86[CHB][hapmap];0.91[JPT][hapmap]
rs6914193	0.83[EUR][1000 genomes]
rs6917432	0.88[EUR][1000 genomes]
rs6921007	0.85[CHB][hapmap];0.95[JPT][hapmap]
rs6921504	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.89[YRI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6925648	0.88[EUR][1000 genomes]
rs6926831	0.85[CEU][hapmap];0.86[CHB][hapmap];0.98[CHD][hapmap];0.91[JPT][hapmap];0.85[MEX][hapmap];0.98[TSI][hapmap];0.85[EUR][1000 genomes]
rs6927748	0.84[CHB][hapmap];0.89[JPT][hapmap]
rs6933046	0.90[CHB][hapmap];0.91[JPT][hapmap]
rs6934603	0.86[CHB][hapmap];0.98[CHD][hapmap];0.91[JPT][hapmap]
rs6940544	0.86[CHB][hapmap];0.91[JPT][hapmap]
rs7739034	0.82[CEU][hapmap];0.81[CHB][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap];0.85[MEX][hapmap];0.98[TSI][hapmap];0.82[EUR][1000 genomes]
rs7739726	0.85[CEU][hapmap];0.91[JPT][hapmap];0.82[EUR][1000 genomes]
rs7742478	0.84[CEU][hapmap];0.81[CHB][hapmap];0.90[JPT][hapmap];0.82[EUR][1000 genomes]
rs7742710	0.90[CHD][hapmap];0.89[JPT][hapmap]
rs7746545	0.88[EUR][1000 genomes]
rs7747129	0.86[EUR][1000 genomes]
rs7748191	0.81[EUR][1000 genomes]
rs7752485	0.85[CEU][hapmap];0.86[CHB][hapmap];0.98[CHD][hapmap];0.91[JPT][hapmap];0.85[MEX][hapmap];0.98[TSI][hapmap];0.83[EUR][1000 genomes]
rs7752882	0.83[EUR][1000 genomes]
rs7755244	0.86[EUR][1000 genomes]
rs7755883	0.85[CHB][hapmap];0.91[JPT][hapmap]
rs7757827	0.89[CEU][hapmap];0.81[CHB][hapmap];0.91[JPT][hapmap];0.80[EUR][1000 genomes]
rs7758618	0.85[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap];0.86[EUR][1000 genomes]
rs7763365	0.82[EUR][1000 genomes]
rs7766324	0.81[CHB][hapmap];0.91[JPT][hapmap];0.82[EUR][1000 genomes]
rs7767449	0.82[EUR][1000 genomes]
rs7768575	0.85[CEU][hapmap];0.81[CHB][hapmap];0.91[JPT][hapmap];0.82[EUR][1000 genomes]
rs7774603	0.86[CHB][hapmap];0.98[CHD][hapmap];0.91[JPT][hapmap]
rs7776407	0.85[CEU][hapmap];0.81[CHB][hapmap];0.91[JPT][hapmap];0.82[EUR][1000 genomes]
rs910563	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.87[JPT][hapmap];0.95[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9344690	0.84[JPT][hapmap];0.82[EUR][1000 genomes]
rs9344691	0.86[CHB][hapmap];0.91[JPT][hapmap]
rs9344693	0.85[CEU][hapmap];0.85[CHB][hapmap];0.91[JPT][hapmap];0.85[EUR][1000 genomes]
rs9344695	0.86[CHB][hapmap];0.98[CHD][hapmap];0.91[JPT][hapmap]
rs9344697	0.88[EUR][1000 genomes]
rs9351117	0.85[CEU][hapmap];0.82[JPT][hapmap];0.82[EUR][1000 genomes]
rs9351124	0.88[EUR][1000 genomes]
rs9353462	0.85[CEU][hapmap];0.81[CHB][hapmap];0.91[JPT][hapmap];0.82[EUR][1000 genomes]
rs9353463	0.82[EUR][1000 genomes]
rs9353464	0.85[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap];0.83[EUR][1000 genomes]
rs9353465	0.85[CEU][hapmap];0.86[CHB][hapmap];0.98[CHD][hapmap];0.91[JPT][hapmap];0.98[TSI][hapmap];0.86[EUR][1000 genomes]
rs9353468	0.86[CHB][hapmap];0.91[JPT][hapmap]
rs9353483	0.88[EUR][1000 genomes]
rs9359743	0.86[CHB][hapmap];0.98[CHD][hapmap];0.91[JPT][hapmap]
rs9359748	0.96[CEU][hapmap];0.95[CHB][hapmap];0.90[MEX][hapmap];0.82[TSI][hapmap];0.88[EUR][1000 genomes]
rs9359749	0.80[EUR][1000 genomes]
rs9362408	0.82[EUR][1000 genomes]
rs9362411	0.90[CHB][hapmap];0.91[JPT][hapmap]
rs9362415	0.86[CHB][hapmap];0.98[CHD][hapmap];0.91[JPT][hapmap]
rs9362427	0.87[EUR][1000 genomes]
rs9444479	0.85[CEU][hapmap];0.81[CHB][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap];0.85[MEX][hapmap];0.98[TSI][hapmap]
rs9450634	0.81[EUR][1000 genomes]
rs9450650	0.85[CHB][hapmap];0.91[JPT][hapmap]
rs9450652	0.86[CHB][hapmap];0.91[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1018155	chr6:88049729-88272862	Strong transcription Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv830722	chr6:88054186-88223625	Enhancers Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs242287	SLC35A1	cis	multi-tissue	Pritchard
rs242287	C6orf162	cis	cerebellum	SCAN
rs242287	C6orf164	cis	Artery Tibial	GTEx
rs242287	C6orf164	cis	Skin Sun Exposed Lower leg	GTEx
rs242287	Hs.485895	cis	multi-tissue	Pritchard
rs242287	C6orf162	cis	parietal	SCAN
rs242287	SLC35A1	cis	parietal	SCAN
rs242287	C6orf164	cis	Thyroid	GTEx
rs242287	ZNF292	cis	Lymphoblastoid	GTEx
rs242287	C6orf164	cis	Whole Blood	GTEx
rs242287	C6orf164	cis	Esophagus Muscularis	GTEx

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:88039000-88078400	Weak transcription	Fetal Stomach	stomach
2	chr6:88040200-88075800	Weak transcription	Fetal Muscle Trunk	muscle
3	chr6:88040600-88116800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr6:88044400-88076000	Weak transcription	Primary hematopoietic stem cells	blood
5	chr6:88044800-88072600	Weak transcription	Adipose Nuclei	Adipose
6	chr6:88044800-88075600	Weak transcription	Fetal Lung	lung
7	chr6:88054800-88075600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr6:88054800-88110200	Weak transcription	Primary T cells from cord blood	blood
9	chr6:88055000-88075800	Weak transcription	Primary B cells from cord blood	blood
10	chr6:88055200-88072800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr6:88057400-88073800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr6:88057600-88077200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr6:88061600-88094600	Weak transcription	Left Ventricle	heart
14	chr6:88063400-88075800	Weak transcription	Aorta	Aorta
15	chr6:88068800-88075800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr6:88069600-88072000	Weak transcription	Stomach Smooth Muscle	stomach
17	chr6:88069800-88075800	Weak transcription	Primary neutrophils fromperipheralblood	blood

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