Variant report

Variant	rs6900111
Chromosome Location	chr6:1941873-1941874
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	chr6:1941619..1944152-chr6:2244261..2246273,2	MCF-7	breast:
2	chr6:1940855..1943499-chr6:1944442..1946843,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000250903	Chromatin interaction
ENSG00000112699	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs12173320	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12175531	1.00[CEU][hapmap];0.89[CHB][hapmap];0.94[JPT][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1323631	1.00[CEU][hapmap];0.89[CHB][hapmap];0.94[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2146920	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3800130	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3800143	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3927456	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6939971	1.00[CEU][hapmap];0.89[CHB][hapmap];0.94[JPT][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9405154	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9405155	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9405533	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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	nsv883384	chr6:1787862-1942538	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	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
8	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
9	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
10	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:39 , 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	chr6:1918600-1946400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr6:1918600-1957800	Weak transcription	Dnd41	blood
8	chr6:1919600-1962400	Weak transcription	Rectal Smooth Muscle	rectum
9	chr6:1924000-1952800	Weak transcription	Fetal Stomach	stomach
10	chr6:1930400-1943400	Weak transcription	Duodenum Mucosa	Duodenum
11	chr6:1930600-1952600	Weak transcription	Fetal Intestine Large	intestine
12	chr6:1932400-1946800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr6:1934800-1943800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr6:1935200-1952200	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr6:1935200-1953800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr6:1935400-1946800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr6:1935400-1953000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr6:1935600-1945200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr6:1935600-1949000	Weak transcription	Primary T cells from cord blood	blood
20	chr6:1935800-1964200	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr6:1936400-1960000	Weak transcription	Primary T helper cells fromperipheralblood	blood
22	chr6:1936800-1958400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
23	chr6:1937000-1942000	Weak transcription	Fetal Intestine Small	intestine
24	chr6:1937000-1949000	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr6:1937400-1961400	Weak transcription	Stomach Mucosa	stomach
26	chr6:1938200-1958400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr6:1940600-1942000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr6:1940600-1942200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr6:1940800-1967200	Weak transcription	Primary B cells from cord blood	blood
30	chr6:1940800-1969800	Weak transcription	Lung	lung
31	chr6:1941000-1949800	Weak transcription	Brain Angular Gyrus	brain
32	chr6:1941000-1952600	Weak transcription	Hela-S3	cervix
33	chr6:1941200-1943000	Weak transcription	GM12878-XiMat	blood
34	chr6:1941400-1942400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr6:1941400-1942600	Strong transcription	HepG2	liver
36	chr6:1941400-1958400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr6:1941600-1942200	Strong transcription	Aorta	Aorta
38	chr6:1941600-1949400	Weak transcription	Brain Substantia Nigra	brain
39	chr6:1941800-1942400	Strong transcription	Rectal Mucosa Donor 29	rectum

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