Variant report

Variant	rs2183067
Chromosome Location	chr6:25015681-25015682
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:25013763..25015712-chr6:25017838..25021035,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-FAM65B-1	chr6:25015181-25015811	ENSG00000251355
2	lnc-GMNN-5	chr6:25013543-25016188	NONHSAT108129
3	lnc-FAM65B-1	chr6:25015180-25015811	ENSG00000272053.1

Extended variants
information (count: 21 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10806997	0.81[CHB][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs10946741	0.90[EUR][1000 genomes]
rs10946742	1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs10946743	0.81[CEU][hapmap];0.84[CHB][hapmap]
rs11758900	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12194111	0.81[JPT][hapmap];1.00[YRI][hapmap]
rs1410689	0.83[TSI][hapmap];0.82[EUR][1000 genomes]
rs1536768	0.81[EUR][1000 genomes]
rs4712878	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4712880	0.81[CEU][hapmap];0.84[CHB][hapmap]
rs6918101	0.84[CEU][hapmap];0.84[CHB][hapmap];0.92[CHD][hapmap]
rs6922006	0.88[EUR][1000 genomes]
rs7748247	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs926850	0.82[ASW][hapmap]
rs983223	0.87[AMR][1000 genomes];0.97[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	nsv1022966	chr6:24763776-25154212	Flanking Active TSS Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv538160	chr6:24763776-25154212	Active TSS Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv883482	chr6:24926730-25035920	Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv1023989	chr6:24930362-25285679	Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Flanking Active TSS 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	43 gene(s)	inside rSNPs	diseases
5	nsv1030634	chr6:24938277-25040161	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
6	nsv830610	chr6:24951741-25124239	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2183067	SLC17A2	cis	parietal	SCAN
rs2183067	CMAH	cis	parietal	SCAN
rs2183067	HIST1H3G	cis	parietal	SCAN

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:24997800-25016600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr6:25007400-25017600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr6:25008000-25016600	Enhancers	Monocytes-CD14+_RO01746	blood
4	chr6:25010000-25016000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr6:25010000-25017400	Enhancers	Hela-S3	cervix
6	chr6:25010000-25018000	Enhancers	HMEC	breast
7	chr6:25010400-25015800	Enhancers	NHLF	lung
8	chr6:25010400-25017200	Enhancers	Osteobl	bone
9	chr6:25011000-25016800	Enhancers	HSMM	muscle
10	chr6:25011200-25023400	Weak transcription	Thymus	Thymus
11	chr6:25011200-25035600	Weak transcription	Spleen	Spleen
12	chr6:25012200-25018400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
13	chr6:25012600-25016800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr6:25012600-25018400	Enhancers	Primary neutrophils fromperipheralblood	blood
15	chr6:25012600-25018600	Enhancers	Primary monocytes fromperipheralblood	blood
16	chr6:25012800-25018600	Enhancers	Primary B cells from peripheral blood	blood
17	chr6:25013000-25016600	Enhancers	Muscle Satellite Cultured Cells	--
18	chr6:25013000-25018200	Enhancers	Primary T helper cells fromperipheralblood	blood
19	chr6:25013200-25017400	Weak transcription	Placenta	Placenta
20	chr6:25013400-25016400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr6:25013600-25015800	Enhancers	GM12878-XiMat	blood
22	chr6:25013600-25017800	Weak transcription	NH-A	brain
23	chr6:25013800-25018400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr6:25014200-25016800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr6:25014200-25018800	Enhancers	Primary B cells from cord blood	blood
26	chr6:25014400-25016000	Enhancers	Rectal Smooth Muscle	rectum
27	chr6:25014400-25018200	Enhancers	Breast Myoepithelial Primary Cells	Breast
28	chr6:25014600-25015800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr6:25014600-25016000	Enhancers	Duodenum Smooth Muscle	Duodenum
30	chr6:25014600-25016000	Enhancers	Pancreatic Islets	Pancreatic Islet
31	chr6:25014600-25017200	Enhancers	Cortex derived primary cultured neurospheres	brain
32	chr6:25014600-25018400	Enhancers	Primary T cells from cord blood	blood
33	chr6:25014800-25015800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr6:25014800-25015800	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
35	chr6:25014800-25015800	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr6:25014800-25015800	Enhancers	Adipose Nuclei	Adipose
37	chr6:25014800-25016000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr6:25014800-25016200	Enhancers	Fetal Lung	lung
39	chr6:25014800-25016600	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr6:25014800-25016800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
41	chr6:25014800-25017000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr6:25014800-25018000	Enhancers	Placenta Amnion	Placenta Amnion
43	chr6:25014800-25018400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr6:25015000-25015800	Genic enhancers	Primary hematopoietic stem cells	blood
45	chr6:25015000-25015800	Enhancers	Brain Angular Gyrus	brain
46	chr6:25015000-25015800	Flanking Active TSS	Brain Germinal Matrix	brain
47	chr6:25015000-25016000	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
48	chr6:25015000-25016000	Enhancers	HSMMtube	muscle
49	chr6:25015000-25018400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
50	chr6:25015200-25015800	Enhancers	Fetal Muscle Leg	muscle

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