Variant report

Variant	rs986883
Chromosome Location	chr3:112317604-112317605
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:112317258..112319990-chr3:112330673..112332621,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SLC35A5-1	chr3:112315667-112322287	XLOC_002759
2	lnc-CCDC80-2	chr3:112315703-112318342	NONHSAT091188
3	lnc-CCDC80-2	chr3:112315641-112320816	NR_109779
4	lnc-CCDC80-2	chr3:112315641-112320749	ENSG00000272761.1

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10934177	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1385527	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1386896	1.00[ASN][1000 genomes]
rs1388442	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1472106	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1472107	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1488260	1.00[ASN][1000 genomes]
rs1488262	1.00[ASN][1000 genomes]
rs1491629	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1532198	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1552707	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1814053	1.00[ASN][1000 genomes]
rs1817694	1.00[ASN][1000 genomes]
rs1844864	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1877362	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1877364	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1906519	1.00[ASN][1000 genomes]
rs2029317	1.00[ASN][1000 genomes]
rs2399431	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2464612	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2638025	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2638030	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2638033	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2638034	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2638036	1.00[ASN][1000 genomes]
rs2638041	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2638043	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2638044	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2668216	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2705506	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2705510	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2705514	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2705520	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2705524	1.00[ASN][1000 genomes]
rs2705551	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2705554	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2705563	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2933139	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2933140	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2969894	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3109033	0.86[ASN][1000 genomes]
rs62264580	0.83[ASN][1000 genomes]
rs6793232	1.00[ASN][1000 genomes]
rs7618978	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs901829	1.00[ASN][1000 genomes]
rs971832	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	nsv877342	chr3:112185025-112332629	Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	esv3329419	chr3:112236688-112620544	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv591301	chr3:112252532-112332629	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112281800-112324200	Weak transcription	Spleen	Spleen
2	chr3:112281800-112325400	Weak transcription	Gastric	stomach
3	chr3:112282000-112330400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr3:112282000-112330600	Weak transcription	Esophagus	oesophagus
5	chr3:112282400-112322800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr3:112282400-112324200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr3:112282400-112340000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr3:112291600-112320600	Weak transcription	NHLF	lung
9	chr3:112293200-112318000	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr3:112298600-112325200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr3:112298800-112335200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr3:112300200-112331000	Weak transcription	Lung	lung
13	chr3:112300200-112334000	Weak transcription	Fetal Stomach	stomach
14	chr3:112302600-112322800	Weak transcription	Colon Smooth Muscle	Colon
15	chr3:112302800-112324200	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr3:112303600-112322800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr3:112303800-112324200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
18	chr3:112304000-112320400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr3:112305000-112324200	Weak transcription	Fetal Brain Male	brain
20	chr3:112305200-112323000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
21	chr3:112305200-112323600	Weak transcription	Brain Substantia Nigra	brain
22	chr3:112305400-112323400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr3:112305400-112324000	Weak transcription	Brain Anterior Caudate	brain
24	chr3:112305400-112330400	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr3:112305600-112324200	Weak transcription	Fetal Kidney	kidney
26	chr3:112305800-112334800	Weak transcription	Aorta	Aorta
27	chr3:112307400-112329000	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr3:112309800-112318200	Weak transcription	Placenta	Placenta
29	chr3:112311600-112330600	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr3:112311600-112331000	Weak transcription	Psoas Muscle	Psoas
31	chr3:112312200-112318000	Weak transcription	Primary neutrophils fromperipheralblood	blood
32	chr3:112312400-112324200	Weak transcription	Ovary	ovary
33	chr3:112312400-112325200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr3:112312400-112326800	Weak transcription	Fetal Lung	lung
35	chr3:112312400-112331000	Weak transcription	HUES64 Cell Line	embryonic stem cell
36	chr3:112312600-112317800	Weak transcription	Primary B cells from peripheral blood	blood
37	chr3:112312600-112318400	Weak transcription	Primary T cells fromperipheralblood	blood
38	chr3:112312600-112322000	Weak transcription	HUVEC	blood vessel
39	chr3:112312600-112323000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr3:112312600-112323400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr3:112312600-112323600	Weak transcription	Primary T helper cells PMA-I stimulated	--
42	chr3:112312600-112323600	Weak transcription	Brain Hippocampus Middle	brain
43	chr3:112312600-112324200	Weak transcription	Brain Angular Gyrus	brain
44	chr3:112312600-112330400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr3:112312600-112346200	Weak transcription	Rectal Smooth Muscle	rectum
46	chr3:112312600-112347200	Weak transcription	Fetal Intestine Large	intestine
47	chr3:112313800-112318000	Strong transcription	Primary B cells from cord blood	blood
48	chr3:112315000-112318000	Strong transcription	Duodenum Smooth Muscle	Duodenum
49	chr3:112315200-112318200	Strong transcription	Fetal Muscle Leg	muscle
50	chr3:112315200-112321000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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