Variant report

Variant	rs2628442
Chromosome Location	chr6:1948868-1948869
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C6orf195-31	chr6:1948760-1949249	NONHSAT106569

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10900914	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11969985	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12524972	0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12528819	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12530211	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12664587	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1570535	0.86[JPT][hapmap]
rs1570537	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17134549	0.93[CEU][hapmap];0.93[CHB][hapmap];0.92[JPT][hapmap];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17134557	0.93[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2281760	0.86[JPT][hapmap]
rs2628443	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2628445	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2628455	1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2761233	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2761235	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3800121	0.87[JPT][hapmap]
rs3800136	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4512269	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4959160	0.86[JPT][hapmap]
rs56031192	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56226194	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62390680	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62391624	0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62391626	0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62391627	0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62391628	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62391632	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6914444	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6916130	0.93[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72841994	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7759192	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7759496	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs912310	0.86[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530548	chr6:1441421-2351608	Weak transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	nsv491607	chr6:1580681-1951526	Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv869043	chr6:1744238-2006788	Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv931941	chr6:1768439-2246781	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS 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	25 gene(s)	inside rSNPs	diseases
5	nsv531295	chr6:1773436-2724986	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription 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	71 gene(s)	inside rSNPs	diseases
6	nsv1032149	chr6:1848148-2006021	Enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv1032727	chr6:1900622-2064690	Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv538095	chr6:1900622-2064690	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	nsv883386	chr6:1910108-2122454	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:1905000-1970600	Weak transcription	Spleen	Spleen
2	chr6:1905400-1962000	Weak transcription	Pancreas	Pancrea
3	chr6:1910200-1965800	Weak transcription	Small Intestine	intestine
4	chr6:1915800-1972800	Weak transcription	Colonic Mucosa	Colon
5	chr6:1916000-1960800	Weak transcription	Gastric	stomach
6	chr6:1918600-1957800	Weak transcription	Dnd41	blood
7	chr6:1919600-1962400	Weak transcription	Rectal Smooth Muscle	rectum
8	chr6:1924000-1952800	Weak transcription	Fetal Stomach	stomach
9	chr6:1930600-1952600	Weak transcription	Fetal Intestine Large	intestine
10	chr6:1935200-1952200	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr6:1935200-1953800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr6:1935400-1953000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr6:1935600-1949000	Weak transcription	Primary T cells from cord blood	blood
14	chr6:1935800-1964200	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr6:1936400-1960000	Weak transcription	Primary T helper cells fromperipheralblood	blood
16	chr6:1936800-1958400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
17	chr6:1937000-1949000	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr6:1937400-1961400	Weak transcription	Stomach Mucosa	stomach
19	chr6:1938200-1958400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr6:1940800-1967200	Weak transcription	Primary B cells from cord blood	blood
21	chr6:1940800-1969800	Weak transcription	Lung	lung
22	chr6:1941000-1949800	Weak transcription	Brain Angular Gyrus	brain
23	chr6:1941000-1952600	Weak transcription	Hela-S3	cervix
24	chr6:1941400-1958400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr6:1941600-1949400	Weak transcription	Brain Substantia Nigra	brain
26	chr6:1942200-1952800	Weak transcription	Aorta	Aorta
27	chr6:1942400-1960800	Weak transcription	Rectal Mucosa Donor 29	rectum
28	chr6:1943600-1952000	Weak transcription	Fetal Intestine Small	intestine
29	chr6:1943600-1966000	Weak transcription	GM12878-XiMat	blood
30	chr6:1944400-1964000	Weak transcription	Primary hematopoietic stem cells	blood
31	chr6:1945600-1961600	Strong transcription	HepG2	liver
32	chr6:1945800-1949000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr6:1946000-1961000	Weak transcription	Left Ventricle	heart
34	chr6:1946000-1964000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr6:1946400-1953400	Strong transcription	Duodenum Mucosa	Duodenum
36	chr6:1946600-1949400	Weak transcription	Primary neutrophils fromperipheralblood	blood
37	chr6:1947200-1949400	Weak transcription	HMEC	breast
38	chr6:1947200-1952600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr6:1947400-1949000	Weak transcription	Adipose Nuclei	Adipose
40	chr6:1947400-1952600	Weak transcription	NHEK	skin
41	chr6:1947400-1980000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
42	chr6:1947800-1956000	Weak transcription	Duodenum Smooth Muscle	Duodenum

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