Variant report

Variant	rs16824139
Chromosome Location	chr2:184061174-184061175
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	chr2:184060293..184062928-chr2:184065628..184067485,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-NUP35-2	chr2:184060294-184061180	NONHSAT075940

Extended variants
information (count: 61 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs1037968	1.00[EUR][1000 genomes]
rs10497623	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11883551	1.00[AMR][1000 genomes]
rs11884352	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11887082	1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11889321	1.00[EUR][1000 genomes]
rs11890612	1.00[EUR][1000 genomes]
rs11890957	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11898922	1.00[EUR][1000 genomes]
rs11899136	1.00[EUR][1000 genomes]
rs11900146	1.00[EUR][1000 genomes]
rs11904544	1.00[EUR][1000 genomes]
rs13422583	1.00[EUR][1000 genomes]
rs1462522	1.00[EUR][1000 genomes]
rs1462523	1.00[EUR][1000 genomes]
rs16823994	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs16824047	1.00[CEU][hapmap];0.94[YRI][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16824100	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16824103	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16824136	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16824141	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16824239	1.00[EUR][1000 genomes]
rs16824259	1.00[EUR][1000 genomes]
rs2045760	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2061657	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs2368356	1.00[EUR][1000 genomes]
rs2368374	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28807996	1.00[EUR][1000 genomes]
rs34386785	1.00[EUR][1000 genomes]
rs55985024	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56987972	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57022552	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58726290	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58782215	1.00[EUR][1000 genomes]
rs59648361	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60159376	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60835883	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60857445	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61190837	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61212352	1.00[EUR][1000 genomes]
rs6434010	1.00[EUR][1000 genomes]
rs6751386	1.00[EUR][1000 genomes]
rs6759272	1.00[EUR][1000 genomes]
rs73040916	1.00[EUR][1000 genomes]
rs73040928	0.88[AFR][1000 genomes]
rs73042731	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73042751	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73042792	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73044730	1.00[EUR][1000 genomes]
rs73050588	1.00[EUR][1000 genomes]
rs73050593	1.00[EUR][1000 genomes]
rs73050598	1.00[EUR][1000 genomes]
rs7584986	1.00[EUR][1000 genomes]
rs898947	1.00[EUR][1000 genomes]
rs955597	1.00[EUR][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	nsv1009882	chr2:183213152-184171519	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv1005281	chr2:183803173-184093877	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv875485	chr2:183827018-184195265	Flanking Active TSS Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
4	nsv1010799	chr2:183855680-184244721	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
5	nsv536072	chr2:183855680-184244721	Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
6	nsv875486	chr2:184016627-184095979	ZNF genes & repeats Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:184015000-184062000	Weak transcription	Small Intestine	intestine
2	chr2:184029200-184062800	Weak transcription	Rectal Smooth Muscle	rectum
3	chr2:184044000-184063000	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr2:184044400-184071600	Weak transcription	NH-A	brain
5	chr2:184047800-184078400	Weak transcription	Colon Smooth Muscle	Colon
6	chr2:184048800-184071800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr2:184049000-184062200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr2:184049000-184072000	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr2:184049000-184072600	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr2:184049000-184078000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr2:184049400-184062600	Weak transcription	HMEC	breast
12	chr2:184050400-184091600	Weak transcription	Psoas Muscle	Psoas
13	chr2:184050600-184066000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr2:184050600-184071400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr2:184050800-184062400	Weak transcription	Brain Hippocampus Middle	brain
16	chr2:184051400-184062600	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr2:184052400-184066200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr2:184052400-184071400	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr2:184052400-184071400	Weak transcription	Aorta	Aorta
20	chr2:184053000-184070200	Weak transcription	Brain Germinal Matrix	brain
21	chr2:184053000-184072000	Weak transcription	Left Ventricle	heart
22	chr2:184053000-184074200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr2:184053200-184076000	Weak transcription	Pancreas	Pancrea
24	chr2:184053800-184062200	Weak transcription	Fetal Intestine Small	intestine
25	chr2:184053800-184064000	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr2:184053800-184067400	Weak transcription	Fetal Muscle Trunk	muscle
27	chr2:184054000-184070600	Weak transcription	HepG2	liver
28	chr2:184054000-184071800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr2:184054000-184076200	Weak transcription	Primary B cells from cord blood	blood
30	chr2:184054600-184062400	Weak transcription	Ovary	ovary
31	chr2:184054600-184067600	Weak transcription	Primary hematopoietic stem cells	blood
32	chr2:184055000-184069200	Weak transcription	Liver	Liver
33	chr2:184055600-184071600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
34	chr2:184055600-184076400	Weak transcription	Primary T cells from cord blood	blood
35	chr2:184055800-184062000	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr2:184056200-184062400	Weak transcription	Adipose Nuclei	Adipose
37	chr2:184056400-184062000	Weak transcription	HSMM	muscle
38	chr2:184056400-184065200	Weak transcription	Primary T helper cells PMA-I stimulated	--
39	chr2:184056600-184062400	Weak transcription	NHEK	skin
40	chr2:184056600-184069200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr2:184056600-184069800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr2:184056800-184061800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
43	chr2:184056800-184062400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr2:184056800-184065800	Weak transcription	Primary T helper cells fromperipheralblood	blood
45	chr2:184056800-184072200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
46	chr2:184056800-184073800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr2:184058400-184069200	Weak transcription	HUES64 Cell Line	embryonic stem cell
48	chr2:184058400-184072400	Weak transcription	Dnd41	blood
49	chr2:184058800-184074200	Weak transcription	A549	lung
50	chr2:184060000-184061800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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