Variant report

Variant	rs2884675
Chromosome Location	chr1:213002088-213002089
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:213001095..213003639-chr1:213003692..213005660,2	K562	blood:
2	chr1:213001465..213003584-chr1:213040615..213043476,2	MCF-7	breast:
3	chr1:213000835..213002742-chr1:213006925..213009621,2	K562	blood:

Extended variants
information (count: 79 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10127613	0.87[EUR][1000 genomes]
rs1032962	0.80[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs1032963	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1032964	0.91[EUR][1000 genomes]
rs1032965	0.81[ASN][1000 genomes]
rs10746436	0.86[LWK][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes]
rs10779583	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10863992	0.84[EUR][1000 genomes]
rs10864002	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[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];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10864003	0.96[YRI][hapmap];0.83[AFR][1000 genomes]
rs11120005	0.84[EUR][1000 genomes]
rs11120028	0.89[ASN][1000 genomes]
rs11120034	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11120038	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12038225	0.98[ASN][1000 genomes]
rs12124669	0.94[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.92[MEX][hapmap];0.84[TSI][hapmap];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12133194	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12239017	0.81[EUR][1000 genomes]
rs12568552	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12744555	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12757944	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1507359	0.91[EUR][1000 genomes]
rs15702	0.94[ASW][hapmap];1.00[CEU][hapmap];0.94[GIH][hapmap];0.95[LWK][hapmap];0.96[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	0.84[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	0.82[ASN][1000 genomes]
rs2456827	0.86[ASN][1000 genomes]
rs3738800	0.89[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs3738802	0.82[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];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4639827	0.91[EUR][1000 genomes]
rs4951464	0.84[ASN][1000 genomes]
rs4951639	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.96[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6540766	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6540767	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[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	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6685864	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6686145	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6686164	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6689799	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[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];0.96[MEX][hapmap];0.84[MKK][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6700465	0.91[EUR][1000 genomes]
rs6702544	0.82[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];0.94[GIH][hapmap];0.88[LWK][hapmap];0.96[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];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[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:14 , 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
5	nsv508691	chr1:212998319-213028392	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	n/a
6	nsv549150	chr1:212999701-213011812	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
7	nsv549151	chr1:213002088-213007296	Enhancers Flanking Active TSS Weak transcription Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
8	nsv549152	chr1:213002088-213007465	Active TSS Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
9	nsv549153	chr1:213002088-213007542	Weak transcription Enhancers Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
10	nsv549154	chr1:213002088-213009469	Weak transcription Flanking Active TSS Enhancers Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
11	nsv549155	chr1:213002088-213009657	Weak transcription Enhancers Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
12	esv2421907	chr1:213002088-213010436	Enhancers Flanking Active TSS Weak transcription Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
13	nsv549156	chr1:213002088-213011812	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
14	nsv549157	chr1:213002088-213018125	Enhancers Flanking Active TSS Active TSS Weak transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs2884675	FLVCR1-AS1	cis	Esophagus Muscularis	GTEx
rs2884675	NEK2	cis	parietal	SCAN
rs2884675	FLVCR1	Cis_1M	lymphoblastoid	RTeQTL
rs2884675	NSL1	cis	lymphoblastoid	seeQTL
rs2884675	FLVCR1-AS1	cis	lung	GTEx
rs2884675	LQK1	Cis_1M	lymphoblastoid	RTeQTL
rs2884675	NCRNA00292	cis	lymphoblastoid	seeQTL
rs2884675	LQK1	cis	cerebellum	SCAN
rs2884675	FLVCR1-AS1	cis	Adipose Subcutaneous	GTEx
rs2884675	NSL1	Cis_1M	lymphoblastoid	RTeQTL
rs2884675	FLVCR1-AS1	cis	Whole Blood	GTEx
rs2884675	LQK1	cis	parietal	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212999400-213009400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr1:212999800-213003600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr1:212999800-213005000	Weak transcription	Adipose Nuclei	Adipose
4	chr1:212999800-213005000	Weak transcription	Monocytes-CD14+_RO01746	blood
5	chr1:213000400-213002800	Enhancers	Fetal Intestine Small	intestine
6	chr1:213000600-213002200	Enhancers	Rectal Mucosa Donor 31	rectum
7	chr1:213000600-213002600	Enhancers	Duodenum Mucosa	Duodenum
8	chr1:213000600-213002800	Enhancers	Fetal Intestine Large	intestine
9	chr1:213000800-213002400	Flanking Active TSS	HepG2	liver
10	chr1:213001000-213005800	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr1:213001400-213004600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr1:213001400-213005800	Weak transcription	A549	lung
13	chr1:213001600-213002200	Enhancers	Sigmoid Colon	Sigmoid Colon
14	chr1:213001800-213008400	Weak transcription	Stomach Mucosa	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links