Variant report

Variant	rs1653626
Chromosome Location	chr1:174739486-174739487
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:17)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

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

No.	Distal block	Cell Line	Cell type
1	chr1:174738363..174739795-chr1:174951924..174953020,9	K562	blood:
2	chr1:174738942..174742917-chr1:174963137..174966746,3	MCF-7	breast:
3	chr1:174738784..174739768-chr1:174967347..174968305,5	K562	blood:
4	chr1:174735208..174740631-chr1:174966337..174969324,7	MCF-7	breast:
5	chr1:174739153..174739796-chr1:174967269..174968128,2	MCF-7	breast:
6	chr1:174738094..174740813-chr1:174741842..174744750,2	K562	blood:
7	chr1:174739087..174740946-chr1:174743005..174745287,2	K562	blood:
8	chr1:174735393..174743353-chr1:174964672..174971853,16	K562	blood:
9	chr1:174737751..174739700-chr1:174991951..174993658,2	MCF-7	breast:
10	chr1:174737719..174739960-chr1:175175568..175177082,2	K562	blood:
11	chr1:174738823..174739778-chr1:174998610..174999515,2	K562	blood:
12	chr1:174738634..174740164-chr1:175067816..175070617,2	K562	blood:
13	chr1:174737447..174741477-chr1:174966880..174970168,5	MCF-7	breast:
14	chr1:174736386..174740944-chr1:174964309..174969947,11	K562	blood:
15	chr1:174566765..174568988-chr1:174739021..174740535,2	K562	blood:
16	chr1:174738859..174740087-chr1:175094536..175095080,4	K562	blood:
17	chr1:174738784..174740555-chr1:174951842..174953064,10	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000120333	Chromatin interaction
ENSG00000252552	Chromatin interaction
ENSG00000116161	Chromatin interaction

Extended variants
information (count: 77 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs1016466	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10753086	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.89[TSI][hapmap];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10912807	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10912813	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10912824	0.85[CEU][hapmap];0.85[GIH][hapmap];0.84[MEX][hapmap]
rs11804541	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11804941	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.89[TSI][hapmap];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12060177	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12074753	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1653627	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.91[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1653632	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs170768	0.85[CEU][hapmap];0.85[GIH][hapmap];0.84[MEX][hapmap]
rs1754349	0.86[EUR][1000 genomes]
rs1754351	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1754355	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1793297	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.91[TSI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1793300	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1793308	0.93[ASN][1000 genomes]
rs1793309	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1793319	0.85[CEU][hapmap];0.85[GIH][hapmap];0.84[MEX][hapmap]
rs2038025	0.88[CEU][hapmap];0.83[MEX][hapmap]
rs2142633	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2187562	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.85[TSI][hapmap];0.86[EUR][1000 genomes]
rs2981894	0.86[EUR][1000 genomes]
rs2987869	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.91[TSI][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2987874	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3018410	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.86[EUR][1000 genomes]
rs3118980	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3133270	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs332765	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs332770	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs332771	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs332773	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs332783	0.84[CEU][hapmap]
rs332789	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs332791	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs332795	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.86[TSI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs332796	0.85[CEU][hapmap];0.85[GIH][hapmap];0.84[MEX][hapmap]
rs332805	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs333418	0.85[CEU][hapmap];0.85[GIH][hapmap];0.84[MEX][hapmap]
rs34819375	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3753563	1.00[CHB][hapmap];0.83[CHD][hapmap];0.91[JPT][hapmap]
rs4233195	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs444678	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs461910	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4650666	0.81[CEU][hapmap]
rs4651238	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.87[MKK][hapmap];0.93[TSI][hapmap]
rs55741955	0.81[EUR][1000 genomes]
rs56347239	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61828140	0.81[EUR][1000 genomes]
rs61828142	0.80[EUR][1000 genomes]
rs6425287	0.83[AFR][1000 genomes];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6425305	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.96[MKK][hapmap];0.93[TSI][hapmap]
rs6658861	0.85[CEU][hapmap];0.85[GIH][hapmap]
rs6664864	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6665216	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.87[MKK][hapmap];0.93[TSI][hapmap]
rs6671824	0.84[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.89[TSI][hapmap];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6672148	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6683602	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.89[TSI][hapmap];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6688577	0.84[ASW][hapmap];0.81[CEU][hapmap];0.85[GIH][hapmap];0.83[MEX][hapmap]
rs6689170	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6696197	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs67967476	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7538588	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.96[MKK][hapmap];0.93[TSI][hapmap];0.81[EUR][1000 genomes]
rs7542389	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7545910	0.82[EUR][1000 genomes]
rs7555533	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.89[TSI][hapmap];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9425784	0.87[ASN][1000 genomes]
rs9628627	0.86[ASN][1000 genomes]
rs9700904	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9804056	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap]
rs989423	1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014637	chr1:174265631-174826765	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv535208	chr1:174265631-174826765	Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	esv2755184	chr1:174388343-174970343	Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
4	nsv548197	chr1:174731596-174741017	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
5	nsv548198	chr1:174731596-174800872	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1653626	C1orf114	cis	cerebellum	SCAN
rs1653626	SLC9A11	cis	parietal	SCAN
rs1653626	PRDX6	cis	parietal	SCAN
rs1653626	MRPS14	cis	parietal	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:174711800-174745600	Weak transcription	Primary B cells from cord blood	blood
2	chr1:174736400-174739800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr1:174737000-174739800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr1:174737600-174741800	Weak transcription	Fetal Intestine Large	intestine
5	chr1:174737600-174744200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr1:174737800-174741800	Weak transcription	Fetal Intestine Small	intestine
7	chr1:174738800-174744400	Enhancers	Liver	Liver
8	chr1:174739400-174739800	Enhancers	HUES64 Cell Line	embryonic stem cell
9	chr1:174739400-174740200	Enhancers	HUES48 Cell Line	embryonic stem cell

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