Variant report

Variant	rs4149506
Chromosome Location	chr2:101032816-101032817
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	chr2:101032545..101035627-chr2:101179557..101182939,4	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-LONRF2-1	chr2:101032685-101032987	NONHSAT072778

Variant related genes	Relation type
ENSG00000115539	Chromatin interaction

Extended variants
information (count: 118 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:112)

rs_ID	r²[population]
rs10167159	0.84[AMR][1000 genomes]
rs10172841	0.86[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs10176978	0.81[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs10180570	0.87[AMR][1000 genomes]
rs10180685	0.86[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs10183063	0.83[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs10184899	0.81[AMR][1000 genomes]
rs10193535	0.90[AMR][1000 genomes]
rs10206374	0.81[AMR][1000 genomes]
rs1057056	0.97[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs1057063	0.97[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs1124009	0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13391930	0.81[AMR][1000 genomes]
rs13396147	0.81[AMR][1000 genomes]
rs13400841	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13404823	0.81[AMR][1000 genomes]
rs13407408	0.81[AMR][1000 genomes]
rs13407648	0.81[AMR][1000 genomes]
rs13407891	0.81[AMR][1000 genomes]
rs13410582	0.81[AMR][1000 genomes]
rs13419808	0.81[AMR][1000 genomes]
rs1347721	0.87[AMR][1000 genomes]
rs1437972	0.90[ASN][1000 genomes]
rs17024034	0.86[ASN][1000 genomes]
rs17024129	0.81[AMR][1000 genomes]
rs17024136	0.81[AMR][1000 genomes]
rs17024144	0.81[AMR][1000 genomes]
rs17024209	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs1898571	0.81[AMR][1000 genomes]
rs1898573	0.88[ASN][1000 genomes]
rs2083148	0.86[ASN][1000 genomes]
rs2309801	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3748936	0.97[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs3791358	0.97[ASN][1000 genomes]
rs4149509	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4149514	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4149515	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4149516	0.85[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs4850932	0.87[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs55640826	0.81[AMR][1000 genomes]
rs55843950	0.81[AMR][1000 genomes]
rs55932868	0.86[ASN][1000 genomes]
rs56118658	0.81[AMR][1000 genomes]
rs56656536	0.90[AMR][1000 genomes]
rs56741959	0.97[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs57862179	0.97[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs58164864	0.97[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs58674788	0.86[ASN][1000 genomes]
rs59701896	0.86[ASN][1000 genomes]
rs59858985	0.86[ASN][1000 genomes]
rs60468180	0.85[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs60566188	0.86[ASN][1000 genomes]
rs60609848	0.90[AMR][1000 genomes]
rs60898093	0.81[AMR][1000 genomes]
rs61321970	0.80[AMR][1000 genomes]
rs61710328	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs6542933	0.86[ASN][1000 genomes]
rs6542945	0.90[ASN][1000 genomes]
rs6542946	0.90[ASN][1000 genomes]
rs6706707	0.86[ASN][1000 genomes]
rs6716009	0.81[AMR][1000 genomes]
rs6716367	0.90[AMR][1000 genomes]
rs6724695	0.81[AMR][1000 genomes]
rs6725672	0.97[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs6728575	0.86[ASN][1000 genomes]
rs6736938	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6738566	0.88[ASN][1000 genomes]
rs6739589	0.90[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6749572	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs6754869	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs6755285	0.97[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs6758161	0.81[AMR][1000 genomes]
rs6758622	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs6761084	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72960184	0.81[AMR][1000 genomes]
rs72960186	0.81[AMR][1000 genomes]
rs72960202	0.81[AMR][1000 genomes]
rs73966105	0.86[ASN][1000 genomes]
rs73966106	0.86[ASN][1000 genomes]
rs73968413	0.86[ASN][1000 genomes]
rs7559084	0.86[ASN][1000 genomes]
rs7559939	0.81[AMR][1000 genomes]
rs7559946	0.81[AMR][1000 genomes]
rs7561065	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7562184	0.86[ASN][1000 genomes]
rs7562461	0.81[AMR][1000 genomes]
rs7562479	0.81[AMR][1000 genomes]
rs7562486	0.81[AMR][1000 genomes]
rs7562615	0.81[AMR][1000 genomes]
rs7562636	0.86[ASN][1000 genomes]
rs7562754	0.86[ASN][1000 genomes]
rs7564178	0.84[AMR][1000 genomes]
rs7565502	0.86[ASN][1000 genomes]
rs7567130	0.88[ASN][1000 genomes]
rs7571410	0.86[ASN][1000 genomes]
rs7571651	0.86[ASN][1000 genomes]
rs7571659	0.86[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs7572119	0.81[AMR][1000 genomes]
rs7574684	0.81[AMR][1000 genomes]
rs7575422	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7576749	0.81[AMR][1000 genomes]
rs7582096	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7582546	0.81[AMR][1000 genomes]
rs7585713	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7585898	0.81[AMR][1000 genomes]
rs7587333	0.93[AMR][1000 genomes]
rs7596483	0.97[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7598205	0.86[ASN][1000 genomes]
rs7598227	0.86[ASN][1000 genomes]
rs7605834	0.86[ASN][1000 genomes]
rs876439	0.86[ASN][1000 genomes]
rs9308834	0.90[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007777	chr2:100816913-101308914	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
2	nsv535844	chr2:100816913-101308914	Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
3	nsv582531	chr2:100908508-101207639	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
4	nsv916792	chr2:101021066-101525200	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
5	nsv582532	chr2:101029002-101531943	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
6	nsv829583	chr2:101031032-101038750	Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:101005800-101033000	Weak transcription	Duodenum Mucosa	Duodenum
2	chr2:101008000-101033000	Weak transcription	Primary T cells fromperipheralblood	blood
3	chr2:101013200-101033000	Weak transcription	Fetal Intestine Large	intestine
4	chr2:101014400-101033200	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr2:101015600-101033000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
6	chr2:101018400-101033000	Weak transcription	Primary B cells from cord blood	blood
7	chr2:101021000-101033200	Weak transcription	Colonic Mucosa	Colon
8	chr2:101022200-101033000	Weak transcription	HSMMtube	muscle
9	chr2:101022800-101033000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr2:101022800-101033000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr2:101023200-101033000	Weak transcription	Primary monocytes fromperipheralblood	blood
12	chr2:101023200-101033000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr2:101023200-101033000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr2:101023200-101033000	Weak transcription	Fetal Thymus	thymus
15	chr2:101023400-101033000	Weak transcription	Fetal Kidney	kidney
16	chr2:101024000-101033000	Weak transcription	Fetal Intestine Small	intestine
17	chr2:101024200-101033000	Weak transcription	Gastric	stomach
18	chr2:101024400-101033000	Weak transcription	Spleen	Spleen
19	chr2:101025000-101033000	Weak transcription	Pancreas	Pancrea
20	chr2:101027000-101033000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr2:101027000-101033000	Weak transcription	Placenta	Placenta
22	chr2:101027000-101033000	Weak transcription	Left Ventricle	heart
23	chr2:101027000-101033000	Weak transcription	Lung	lung
24	chr2:101027000-101033000	Weak transcription	Right Ventricle	heart
25	chr2:101027000-101033200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr2:101028000-101033000	Enhancers	Brain Substantia Nigra	brain
27	chr2:101029000-101033000	Weak transcription	Aorta	Aorta
28	chr2:101029600-101033000	Weak transcription	Placenta Amnion	Placenta Amnion
29	chr2:101030000-101033000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr2:101030800-101033000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr2:101030800-101033000	Weak transcription	Fetal Muscle Trunk	muscle
32	chr2:101031000-101033000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr2:101031000-101033000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr2:101031000-101033200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
35	chr2:101032000-101033000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
36	chr2:101032000-101033000	Active TSS	Primary T cells from cord blood	blood
37	chr2:101032000-101033600	Flanking Active TSS	Dnd41	blood
38	chr2:101032200-101033000	Enhancers	Rectal Smooth Muscle	rectum
39	chr2:101032200-101033600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr2:101032200-101034400	Active TSS	Brain Angular Gyrus	brain
41	chr2:101032200-101034600	Active TSS	Ovary	ovary
42	chr2:101032400-101033000	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
43	chr2:101032400-101033000	Enhancers	Breast Myoepithelial Primary Cells	Breast
44	chr2:101032400-101033200	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
45	chr2:101032400-101033200	Enhancers	Primary T helper cells PMA-I stimulated	--
46	chr2:101032400-101033400	Flanking Active TSS	Brain Anterior Caudate	brain
47	chr2:101032400-101033400	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
48	chr2:101032400-101034400	Active TSS	GM12878-XiMat	blood
49	chr2:101032400-101034400	Active TSS	K562	blood
50	chr2:101032600-101033000	Active TSS	H1 Cell Line	embryonic stem cell

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