Variant report

Variant	rs10864002
Chromosome Location	chr1:212997385-212997386
allele	C/T
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:15)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

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

No.	Distal block	Cell Line	Cell type
1	chr1:212995878..212997398-chr17:41463374..41466194,3	K562	blood:
2	chr1:212995878..212997398-chr17:41380725..41383268,2	MCF-7	breast:
3	chr1:212995878..212997398-chr3:73159960..73162072,6	K562	blood:
4	chr1:212964912..212966461-chr1:212995791..212998620,2	K562	blood:
5	chr1:212995898..212997398-chr11:62607619..62609127,2	K562	blood:
6	chr1:212995898..212997398-chr11:62607627..62609133,2	K562	blood:
7	chr1:212995878..212997398-chr3:73160015..73162089,7	MCF-7	breast:
8	chr1:212997378..212998898-chr17:41399483..41402356,3	K562	blood:
9	chr1:212996878..212997398-chr11:62608628..62609644,4	HCT-116	colon:
10	chr1:212997378..212997898-chr3:73160072..73160592,2	Hela-S3	cervix:
11	chr1:212995878..212997398-chr17:41380306..41382306,2	K562	blood:
12	chr1:212996878..212997398-chr3:73159952..73160630,6	HCT-116	colon:
13	chr1:212995878..212997398-chr3:73160094..73162072,3	K562	blood:
14	chr1:212996878..212997398-chr3:73159633..73160628,4	NB4	blood:
15	chr1:212997378..212997898-chr11:5382283..5382803,2	HCT-116	colon:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TATDN3-1	chr1:212997369-212997847	NONHSAT009402

No data

Variant related genes	Relation type
ENSG00000203705	Chromatin interaction
ENSG00000133316	Chromatin interaction
ENSG00000223247	Chromatin interaction
ENSG00000188825	Chromatin interaction
ENSG00000117697	Chromatin interaction
ENSG00000236383	Chromatin interaction

Extended variants
information (count: 72 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10127613	0.87[EUR][1000 genomes]
rs1021994	0.80[ASN][1000 genomes]
rs1032962	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs1032963	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1032964	0.91[EUR][1000 genomes]
rs1032965	0.84[ASN][1000 genomes]
rs10746436	0.86[LWK][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes]
rs10779583	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10863992	0.84[EUR][1000 genomes]
rs10864003	0.96[YRI][hapmap];0.84[AFR][1000 genomes]
rs11120005	0.84[EUR][1000 genomes]
rs11120028	0.89[ASN][1000 genomes]
rs11120033	0.81[AFR][1000 genomes]
rs11120034	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11120038	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12038225	0.95[ASN][1000 genomes]
rs12124669	0.94[ASW][hapmap];0.90[CHB][hapmap];0.92[CHD][hapmap];0.94[GIH][hapmap];0.83[MEX][hapmap];0.82[TSI][hapmap];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12133194	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12239017	0.81[EUR][1000 genomes]
rs12568552	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12744555	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];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12757944	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1507359	0.91[EUR][1000 genomes]
rs15702	0.94[ASW][hapmap];1.00[CEU][hapmap];0.97[GIH][hapmap];0.95[LWK][hapmap];0.87[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.91[EUR][1000 genomes]
rs1580991	0.83[EUR][1000 genomes]
rs1580992	0.83[EUR][1000 genomes]
rs1605420	0.80[EUR][1000 genomes]
rs1813705	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1848243	0.89[EUR][1000 genomes]
rs2292214	0.88[EUR][1000 genomes]
rs2456818	0.85[ASN][1000 genomes]
rs2456827	0.89[ASN][1000 genomes]
rs2456828	0.81[ASN][1000 genomes]
rs2884675	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3738800	0.90[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs3738802	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3949369	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4639827	0.91[EUR][1000 genomes]
rs4951464	0.87[ASN][1000 genomes]
rs4951639	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.87[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6540766	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6540767	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6665489	0.83[EUR][1000 genomes]
rs6670373	0.83[EUR][1000 genomes]
rs6670869	0.90[EUR][1000 genomes]
rs6678961	0.83[EUR][1000 genomes]
rs6681851	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6685864	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6686145	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6686164	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6689799	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6694887	0.91[EUR][1000 genomes]
rs6696870	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.87[MEX][hapmap];0.84[MKK][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6700465	0.91[EUR][1000 genomes]
rs6702544	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6703982	0.83[EUR][1000 genomes]
rs7513199	0.89[EUR][1000 genomes]
rs7513210	0.89[EUR][1000 genomes]
rs7513734	0.89[EUR][1000 genomes]
rs7513772	0.89[EUR][1000 genomes]
rs7514070	0.83[ASW][hapmap];1.00[CEU][hapmap];0.97[GIH][hapmap];0.88[LWK][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes]
rs7522100	0.91[EUR][1000 genomes]
rs7528303	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7535608	0.91[EUR][1000 genomes]
rs7538853	0.91[EUR][1000 genomes]
rs7543603	0.89[EUR][1000 genomes]
rs7547100	0.89[EUR][1000 genomes]
rs7555930	0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001637	chr1:212907611-213034606	Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
2	esv2756884	chr1:212925429-213006397	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
3	esv2758997	chr1:212925429-213006397	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
4	nsv549149	chr1:212997385-213009657	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats	Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	n/a

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs10864002	LQK1	cis	parietal	SCAN
rs10864002	FLVCR1-AS1	cis	Esophagus Muscularis	GTEx
rs10864002	NSL1	cis	lymphoblastoid	seeQTL
rs10864002	LQK1	cis	cerebellum	SCAN
rs10864002	FLVCR1-AS1	cis	Adipose Subcutaneous	GTEx
rs10864002	NEK2	cis	parietal	SCAN
rs10864002	LQK1	Cis_1M	lymphoblastoid	RTeQTL
rs10864002	FLVCR1-AS1	cis	Whole Blood	GTEx
rs10864002	FLVCR1-AS1	cis	lung	GTEx
rs10864002	TATDN3	cis	multi-tissue	Pritchard
rs10864002	NSL1	Cis_1M	lymphoblastoid	RTeQTL
rs10864002	NCRNA00292	cis	lymphoblastoid	seeQTL
rs10864002	FLVCR1	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212966000-212997400	Weak transcription	Aorta	Aorta
2	chr1:212975800-212997800	Weak transcription	Brain Substantia Nigra	brain
3	chr1:212976200-212998800	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr1:212979600-213001000	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr1:212980800-213001000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr1:212988400-212998800	Weak transcription	Adipose Nuclei	Adipose
7	chr1:212988600-212998400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr1:212990800-212998600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr1:212991000-212998800	Weak transcription	Stomach Mucosa	stomach
10	chr1:212994000-212999000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr1:212996200-212997400	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr1:212996400-212998600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr1:212997000-212998600	Weak transcription	HepG2	liver
14	chr1:212997200-212997400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr1:212997200-213000200	ZNF genes & repeats	Fetal Intestine Small	intestine

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