Variant report

Variant	rs11120005
Chromosome Location	chr1:212895973-212895974
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:212873103..212876136-chr1:212895227..212897615,4	K562	blood:
2	chr1:212890618..212893441-chr1:212895011..212896992,2	K562	blood:
3	chr1:212883928..212885443-chr1:212893940..212896251,2	K562	blood:

Variant related genes	Relation type
ENSG00000123685	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10127613	0.90[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs1032964	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10779582	0.96[ASN][1000 genomes]
rs10779583	0.85[EUR][1000 genomes]
rs10863992	0.86[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs10864002	0.84[EUR][1000 genomes]
rs11120034	0.84[EUR][1000 genomes]
rs12133194	0.80[EUR][1000 genomes]
rs12239017	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12568552	0.86[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs12744555	0.84[EUR][1000 genomes]
rs12757944	0.84[EUR][1000 genomes]
rs1507359	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs15702	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1580991	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1580992	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1605420	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1813705	0.86[EUR][1000 genomes]
rs1848243	0.98[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2292214	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2884675	0.84[EUR][1000 genomes]
rs3738802	0.93[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs3949369	0.84[EUR][1000 genomes]
rs4548508	0.97[ASN][1000 genomes]
rs4639827	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4951458	0.97[ASN][1000 genomes]
rs4951639	0.89[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs6540754	0.84[ASN][1000 genomes]
rs6540766	0.86[EUR][1000 genomes]
rs6540767	0.84[EUR][1000 genomes]
rs6665489	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6670373	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6670869	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6678961	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6681851	0.80[EUR][1000 genomes]
rs6685864	0.80[EUR][1000 genomes]
rs6686164	0.87[EUR][1000 genomes]
rs6688947	0.97[ASN][1000 genomes]
rs6694887	0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6696870	0.80[EUR][1000 genomes]
rs6696908	0.83[AMR][1000 genomes]
rs6700465	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6702544	0.89[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs6703982	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7513199	0.90[EUR][1000 genomes]
rs7513210	0.90[EUR][1000 genomes]
rs7513734	0.95[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs7513772	0.95[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs7514070	0.98[AFR][1000 genomes];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7522100	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7528303	0.84[EUR][1000 genomes]
rs7535608	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7538853	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7543603	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7547100	0.95[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs7555930	0.85[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs9651103	0.93[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	nsv1013110	chr1:212555764-212948092	Flanking Active TSS Bivalent/Poised TSS Strong transcription Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	81 gene(s)	inside rSNPs	diseases
2	nsv535287	chr1:212555764-212948092	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	81 gene(s)	inside rSNPs	diseases
3	nsv549148	chr1:212876902-212962207	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs11120005	NSL1	Cis_1M	lymphoblastoid	RTeQTL
rs11120005	FLVCR1-AS1	cis	Esophagus Muscularis	GTEx
rs11120005	FLVCR1	Cis_1M	lymphoblastoid	RTeQTL
rs11120005	FLVCR1-AS1	cis	Whole Blood	GTEx
rs11120005	LQK1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212894400-212897200	Enhancers	Primary hematopoietic stem cells short term culture	blood
2	chr1:212894600-212896000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
3	chr1:212894600-212896200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
4	chr1:212894600-212896200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr1:212894600-212896400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
6	chr1:212894600-212896400	Enhancers	HUVEC	blood vessel
7	chr1:212894600-212897200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr1:212894600-212897200	Enhancers	Dnd41	blood
9	chr1:212894800-212896000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr1:212895000-212896200	Enhancers	Primary monocytes fromperipheralblood	blood
11	chr1:212895000-212896400	Enhancers	Monocytes-CD14+_RO01746	blood
12	chr1:212895200-212922800	Weak transcription	Left Ventricle	heart
13	chr1:212895400-212896000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr1:212895400-212896800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr1:212895400-212897400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
16	chr1:212895400-212897400	Enhancers	HepG2	liver
17	chr1:212895400-212899800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr1:212895400-212901800	Weak transcription	Liver	Liver
19	chr1:212895400-212902000	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr1:212895400-212902400	Weak transcription	Primary T cells from cord blood	blood
21	chr1:212895400-212906000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr1:212895400-212906600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
23	chr1:212895400-212912000	Weak transcription	Primary T cells fromperipheralblood	blood
24	chr1:212895400-212914600	Weak transcription	Spleen	Spleen
25	chr1:212895400-212916600	Weak transcription	Primary T helper cells fromperipheralblood	blood
26	chr1:212895400-212917400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr1:212895400-212923200	Weak transcription	Brain Cingulate Gyrus	brain
28	chr1:212895400-212923400	Weak transcription	Fetal Muscle Leg	muscle
29	chr1:212895400-212923400	Weak transcription	Skeletal Muscle Female	skeletal muscle
30	chr1:212895400-212926400	Weak transcription	Esophagus	oesophagus
31	chr1:212895400-212964600	Weak transcription	Pancreas	Pancrea
32	chr1:212895600-212896000	Weak transcription	Duodenum Mucosa	Duodenum
33	chr1:212895600-212896200	Enhancers	Primary neutrophils fromperipheralblood	blood
34	chr1:212895600-212896200	Enhancers	K562	blood
35	chr1:212895600-212897400	Weak transcription	HSMM	muscle
36	chr1:212895600-212899800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr1:212895600-212900000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr1:212895600-212900400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr1:212895600-212900400	Weak transcription	Osteobl	bone
40	chr1:212895600-212900600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr1:212895600-212900600	Weak transcription	NH-A	brain
42	chr1:212895600-212901000	Weak transcription	Muscle Satellite Cultured Cells	--
43	chr1:212895600-212904000	Weak transcription	GM12878-XiMat	blood
44	chr1:212895600-212905600	Weak transcription	Lung	lung
45	chr1:212895600-212923000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr1:212895600-212923400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr1:212895600-212964600	Weak transcription	Gastric	stomach
48	chr1:212895800-212896800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr1:212895800-212897400	Enhancers	A549	lung
50	chr1:212895800-212900200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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