Variant report

Variant	rs4653584
Chromosome Location	chr1:224541645-224541646
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	KAP1	chr1:224541580-224542437	HEK293	kidney:	n/a	n/a
2	CBX3	chr1:224541601-224542185	K562	blood:	n/a	n/a
3	FOXA1	chr1:224541629-224541945	HepG2	liver:	n/a	n/a
4	KAP1	chr1:224541579-224542184	U2OS	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:224528975..224532338-chr1:224541098..224544452,3	K562	blood:

Variant related genes	Relation type
CNIH4	TF binding region

Extended variants
information (count: 99 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:96)

rs_ID	r²[population]
rs10158063	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs10733024	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10737442	0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10737443	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10753462	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10753464	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10799562	0.85[CEU][hapmap];0.89[CHB][hapmap];0.94[CHD][hapmap];0.92[GIH][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10799563	0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10799566	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10799567	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10799568	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10916577	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10916585	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.97[LWK][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10916599	0.80[ASN][1000 genomes]
rs11802486	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11811730	0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16846031	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16846094	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16846214	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16846244	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1806742	1.00[CHB][hapmap];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2001712	0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2001713	0.92[EUR][1000 genomes]
rs2404783	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2404856	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2404857	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2404858	0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2404859	0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2404861	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2405062	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2405065	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2405067	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2405070	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2896990	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2896992	0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2897054	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3754090	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3767721	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3767722	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.87[TSI][hapmap];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3767723	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3767724	0.98[ASN][1000 genomes]
rs3767725	0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4146965	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4146966	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4233234	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4233235	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[TSI][hapmap]
rs4256779	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4420060	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4457542	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4628473	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4653575	0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4653579	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];0.82[JPT][hapmap];0.97[LWK][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4653580	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.94[LWK][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4653581	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4653583	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4654011	0.86[ASN][1000 genomes]
rs4654017	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4654019	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4654022	0.89[CHB][hapmap];0.98[ASN][1000 genomes]
rs4654023	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4654032	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4654033	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4654034	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55675086	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55980628	0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57324770	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58855990	0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59106681	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6426088	0.89[CHB][hapmap];0.94[CHD][hapmap];0.82[JPT][hapmap];0.89[ASN][1000 genomes]
rs6426094	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6426100	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs6426110	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6426114	0.93[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6426115	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6426117	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6681790	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6682667	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6685600	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6691689	0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6694745	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6696795	0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6699017	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73118046	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73128468	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73130436	0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73130448	0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73130455	0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73130462	0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73130464	0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7521015	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7522392	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7529143	0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7530205	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7534101	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7534447	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9287027	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[EUR][1000 genomes];0.89[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	nsv8868	chr1:224383023-224752531	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv469889	chr1:224440354-224634374	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
3	nsv482318	chr1:224440354-224634374	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4653584	NVL	cis	multi-tissue	Pritchard

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:224529200-224544000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr1:224536800-224544200	Weak transcription	Primary T helper cells PMA-I stimulated	--
3	chr1:224536800-224544400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr1:224536800-224544600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr1:224538400-224544400	Weak transcription	Right Atrium	heart
6	chr1:224540600-224544400	Enhancers	Fetal Intestine Small	intestine
7	chr1:224540800-224542000	Enhancers	Duodenum Mucosa	Duodenum
8	chr1:224540800-224544400	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr1:224540800-224544400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr1:224540800-224544400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr1:224541200-224544200	Enhancers	Rectal Mucosa Donor 31	rectum
12	chr1:224541200-224544400	Enhancers	Fetal Intestine Large	intestine
13	chr1:224541400-224541800	Active TSS	Rectal Mucosa Donor 29	rectum
14	chr1:224541400-224542400	Enhancers	Primary T cells from cord blood	blood
15	chr1:224541600-224543200	Enhancers	HepG2	liver

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