Variant report

Variant	rs6696239
Chromosome Location	chr1:227750068-227750069
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	chr1:227126771..227129566-chr1:227749760..227753054,3	K562	blood:

Variant related genes	Relation type
ENSG00000163050	Chromatin interaction

Extended variants
information (count: 93 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs1045407	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10753436	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10753437	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10799422	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10799424	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10799428	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10799437	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10799444	1.00[CHB][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes]
rs10916154	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10916157	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10916160	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10916161	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10916162	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10916163	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10916166	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10916167	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.89[MEX][hapmap];0.98[MKK][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10916173	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10916180	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10916189	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10916199	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11576992	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11581704	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11590390	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12058246	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12081818	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12084072	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12092054	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12093031	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12097239	0.86[ASW][hapmap];0.85[MKK][hapmap]
rs12116848	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12119889	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12120182	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12123996	0.81[ASW][hapmap];0.90[CEU][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12129704	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12129894	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12131114	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12132761	0.81[EUR][1000 genomes]
rs12133625	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12138198	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12138229	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12140813	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12140848	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1390401	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];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1495848	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1845757	0.87[EUR][1000 genomes]
rs1995019	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2172936	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28446171	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2999742	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34421331	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3942992	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4379651	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57158394	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs59885016	0.81[EUR][1000 genomes]
rs61824940	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6426470	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6426471	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6426472	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6656661	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6659012	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6659349	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6669236	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6669277	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6672530	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6678802	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6679855	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6689375	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6691443	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6692376	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6694427	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6698409	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs74140304	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7418348	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7521812	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7531801	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7538206	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7538893	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7540382	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7549475	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7551788	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7553531	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs903691	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs951084	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9726691	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.96[TSI][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][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	nsv534002	chr1:227315186-228047108	Bivalent/Poised TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
2	esv2753828	chr1:227670265-227791265	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv873246	chr1:227694948-227884465	Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Strong transcription 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
4	nsv1007479	chr1:227695868-227984466	Genic enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
5	nsv873248	chr1:227710381-227786033	ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
6	nsv947520	chr1:227724042-227750192	Weak transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
7	nsv947560	chr1:227726600-227750192	ZNF genes & repeats Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
8	esv3338615	chr1:227738421-227798486	Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	esv3327012	chr1:227741102-227890968	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6696239	TAF5L	cis	parietal	SCAN
rs6696239	JMJD4	cis	multi-tissue	Pritchard
rs6696239	ZNF678	Cis_1M	lymphoblastoid	RTeQTL
rs6696239	ZNF678	cis	cerebellum	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227746400-227751200	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
2	chr1:227748200-227750800	Weak transcription	Brain Substantia Nigra	brain
3	chr1:227748600-227750800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr1:227749000-227750800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr1:227749000-227750800	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr1:227749000-227750800	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr1:227749000-227750800	Weak transcription	Right Atrium	heart
8	chr1:227749200-227750800	Weak transcription	Right Ventricle	heart
9	chr1:227749800-227750800	Weak transcription	Spleen	Spleen
10	chr1:227749800-227751000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr1:227750000-227750200	ZNF genes & repeats	Pancreas	Pancrea
12	chr1:227750000-227751000	ZNF genes & repeats	Dnd41	blood

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