Variant report

Variant	rs1004868
Chromosome Location	chr2:231038910-231038911
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:231033479..231035514-chr2:231038836..231041056,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SP140-3	chr2:231038404-231038939	NONHSAT077267
2	lnc-SP140-3	chr2:231038404-231038939	ENSG00000225963.3

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1004869	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap]
rs10165012	1.00[CHB][hapmap]
rs10170241	1.00[CHB][hapmap]
rs12988385	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12995739	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs13010639	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13010998	0.88[CEU][hapmap];1.00[CHB][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13018234	0.89[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13025209	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13025520	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13026323	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1427293	1.00[CHB][hapmap]
rs1427294	1.00[CHB][hapmap]
rs2114585	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2162478	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34034766	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34122378	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34897866	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35574529	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35849510	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3948464	1.00[CHB][hapmap]
rs41309106	1.00[ASN][1000 genomes]
rs41543719	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6707444	1.00[CHB][hapmap]
rs6710287	1.00[CHB][hapmap]
rs6742304	1.00[CHB][hapmap]
rs9783992	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9783994	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9784019	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007920	chr2:230775427-231065592	Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv1001562	chr2:230862717-231187043	Flanking Active TSS ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv536156	chr2:230862717-231187043	Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	nsv498047	chr2:230951712-231250489	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:231025000-231040000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
2	chr2:231026400-231041600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr2:231026400-231041800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr2:231026600-231040200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr2:231026600-231041400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr2:231028400-231067000	Strong transcription	Primary B cells from peripheral blood	blood
7	chr2:231028600-231039600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr2:231028600-231051200	Strong transcription	Primary T helper cells fromperipheralblood	blood
9	chr2:231028800-231051600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr2:231030800-231051000	Strong transcription	Primary T cells fromperipheralblood	blood
11	chr2:231030800-231051000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr2:231031000-231040600	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr2:231031200-231049800	Weak transcription	HSMMtube	muscle
14	chr2:231031400-231051000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr2:231031400-231051000	Strong transcription	Fetal Thymus	thymus
16	chr2:231031400-231051600	Strong transcription	GM12878-XiMat	blood
17	chr2:231031400-231061200	Strong transcription	Primary B cells from cord blood	blood
18	chr2:231031600-231050800	Strong transcription	Fetal Muscle Leg	muscle
19	chr2:231031600-231052400	Weak transcription	Fetal Brain Male	brain
20	chr2:231031800-231049400	Strong transcription	Liver	Liver
21	chr2:231032800-231039000	Weak transcription	Left Ventricle	heart
22	chr2:231033800-231050800	Strong transcription	Dnd41	blood
23	chr2:231034200-231041800	Weak transcription	Colonic Mucosa	Colon
24	chr2:231034800-231047400	Weak transcription	Small Intestine	intestine
25	chr2:231035000-231051800	Strong transcription	Primary T cells from cord blood	blood
26	chr2:231035200-231044600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
27	chr2:231035400-231039200	Weak transcription	Rectal Smooth Muscle	rectum
28	chr2:231035400-231039400	Weak transcription	Brain Cingulate Gyrus	brain
29	chr2:231035400-231041200	Weak transcription	Rectal Mucosa Donor 31	rectum
30	chr2:231035400-231077000	Weak transcription	HepG2	liver
31	chr2:231035600-231041600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr2:231035600-231042000	Weak transcription	Brain Substantia Nigra	brain
33	chr2:231035600-231042200	Weak transcription	Stomach Mucosa	stomach
34	chr2:231035600-231049000	Weak transcription	Brain Angular Gyrus	brain
35	chr2:231035600-231050400	Strong transcription	Primary monocytes fromperipheralblood	blood
36	chr2:231035600-231050400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
37	chr2:231035600-231050800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
38	chr2:231035600-231050800	Strong transcription	Thymus	Thymus
39	chr2:231035600-231051000	Strong transcription	Primary neutrophils fromperipheralblood	blood
40	chr2:231035600-231051000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr2:231035600-231051200	Strong transcription	Monocytes-CD14+_RO01746	blood
42	chr2:231035600-231051600	Strong transcription	Primary T helper cells PMA-I stimulated	--
43	chr2:231035800-231042000	Weak transcription	Brain Anterior Caudate	brain
44	chr2:231035800-231049600	Weak transcription	Brain Inferior Temporal Lobe	brain
45	chr2:231035800-231062800	Weak transcription	Muscle Satellite Cultured Cells	--
46	chr2:231036000-231048400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr2:231036200-231048800	Strong transcription	Lung	lung
48	chr2:231036200-231049200	Strong transcription	Adipose Nuclei	Adipose
49	chr2:231036200-231050800	Strong transcription	Duodenum Smooth Muscle	Duodenum
50	chr2:231036200-231051200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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