Variant report

Variant	rs11120038
Chromosome Location	chr1:213004406-213004407
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:213001095..213003639-chr1:213003692..213005660,2	K562	blood:

Extended variants
information (count: 84 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10127613	0.83[EUR][1000 genomes]
rs1032962	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1032963	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1032964	0.86[EUR][1000 genomes]
rs10746436	0.81[AFR][1000 genomes]
rs10779583	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10864002	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10864003	0.81[AFR][1000 genomes]
rs11120028	0.88[ASN][1000 genomes]
rs11120034	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11120043	0.81[AMR][1000 genomes]
rs12038225	0.99[ASN][1000 genomes]
rs12124669	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12133194	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12568552	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12744555	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12757944	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1507359	0.87[EUR][1000 genomes]
rs15702	0.87[EUR][1000 genomes]
rs1813705	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1848243	0.85[EUR][1000 genomes]
rs2292214	0.84[EUR][1000 genomes]
rs2456818	0.81[ASN][1000 genomes]
rs2456827	0.85[ASN][1000 genomes]
rs2884675	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3738800	0.88[ASN][1000 genomes]
rs3738802	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3949369	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4639827	0.86[EUR][1000 genomes]
rs4951464	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4951639	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6540766	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6540767	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6670869	0.86[EUR][1000 genomes]
rs6681851	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6685864	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6686145	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6686164	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6689799	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6694887	0.86[EUR][1000 genomes]
rs6696870	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6696908	0.81[EUR][1000 genomes]
rs6700465	0.87[EUR][1000 genomes]
rs6702544	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7513199	0.85[EUR][1000 genomes]
rs7513210	0.85[EUR][1000 genomes]
rs7513734	0.85[EUR][1000 genomes]
rs7513772	0.85[EUR][1000 genomes]
rs7514070	0.85[EUR][1000 genomes]
rs7522100	0.87[EUR][1000 genomes]
rs7528303	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7535608	0.86[EUR][1000 genomes]
rs7538853	0.86[EUR][1000 genomes]
rs7543603	0.85[EUR][1000 genomes]
rs7547100	0.85[EUR][1000 genomes]
rs7555930	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:28 , 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
15	nsv8791	chr1:213002097-213014844	Weak transcription Enhancers Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
16	esv3321128	chr1:213002226-213013781	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
17	nsv826564	chr1:213002232-213013565	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
18	esv3321127	chr1:213002235-213013744	Enhancers Flanking Active TSS Weak transcription Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
19	esv3321126	chr1:213002278-213013753	Weak transcription Enhancers Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
20	esv3321130	chr1:213002280-213013711	Enhancers Weak transcription Active TSS Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
21	esv3349041	chr1:213002330-213013685	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
22	esv3321131	chr1:213002369-213013669	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
23	nsv549158	chr1:213003428-213007542	Enhancers Flanking Active TSS Weak transcription Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
24	nsv549159	chr1:213003428-213008227	Weak transcription Flanking Active TSS Enhancers Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
25	nsv549160	chr1:213003428-213009469	Weak transcription Enhancers Active TSS Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
26	nsv549161	chr1:213003428-213009657	Weak transcription Enhancers Active TSS Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
27	nsv549162	chr1:213003428-213011812	Active TSS Weak transcription Flanking Active TSS Enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
28	nsv549163	chr1:213003428-213018125	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs11120038	NSL1	Cis_1M	lymphoblastoid	RTeQTL
rs11120038	FLVCR1-AS1	cis	Whole Blood	GTEx
rs11120038	FLVCR1	Cis_1M	lymphoblastoid	RTeQTL
rs11120038	FLVCR1-AS1	cis	lung	GTEx
rs11120038	FLVCR1-AS1	cis	Esophagus Muscularis	GTEx
rs11120038	LQK1	Cis_1M	lymphoblastoid	RTeQTL
rs11120038	FLVCR1-AS1	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:13 , 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	chr1:212999800-213005000	Weak transcription	Adipose Nuclei	Adipose
3	chr1:212999800-213005000	Weak transcription	Monocytes-CD14+_RO01746	blood
4	chr1:213001000-213005800	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr1:213001400-213004600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr1:213001400-213005800	Weak transcription	A549	lung
7	chr1:213001800-213008400	Weak transcription	Stomach Mucosa	stomach
8	chr1:213002200-213006200	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr1:213002600-213006000	Weak transcription	Duodenum Mucosa	Duodenum
10	chr1:213002800-213005800	Weak transcription	Fetal Intestine Small	intestine
11	chr1:213002800-213006000	Weak transcription	Fetal Intestine Large	intestine
12	chr1:213002800-213006000	Weak transcription	HepG2	liver
13	chr1:213002800-213006400	Weak transcription	Rectal Mucosa Donor 31	rectum

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