Variant report

Variant	rs216260
Chromosome Location	chr6:24931053-24931054
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:24929367..24931167-chr6:24936238..24937978,2	MCF-7	breast:
2	chr6:24930706..24933107-chr6:24936123..24938054,3	K562	blood:

Variant related genes	Relation type
ENSG00000111913	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs12202529	1.00[CHB][hapmap];0.82[JPT][hapmap];0.89[ASN][1000 genomes]
rs12216261	0.89[ASN][1000 genomes]
rs1626145	0.82[ASN][1000 genomes]
rs16889835	0.93[CHB][hapmap];0.82[ASN][1000 genomes]
rs1753511	0.84[ASN][1000 genomes]
rs1813711	0.83[ASN][1000 genomes]
rs216256	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs216257	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs216258	0.84[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs216261	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs216262	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs370748	0.84[ASN][1000 genomes]
rs386511	0.84[ASN][1000 genomes]
rs388071	0.84[ASN][1000 genomes]
rs413203	0.89[ASN][1000 genomes]
rs413610	0.84[ASN][1000 genomes]
rs415025	0.84[ASN][1000 genomes]
rs419288	0.85[ASN][1000 genomes]
rs421817	0.83[CHB][hapmap];0.83[JPT][hapmap];0.84[ASN][1000 genomes]
rs431796	0.84[ASN][1000 genomes]
rs432593	0.84[ASN][1000 genomes]
rs495157	0.83[CHB][hapmap];0.83[JPT][hapmap]
rs628794	0.83[CHB][hapmap];0.83[JPT][hapmap];0.84[ASN][1000 genomes]
rs640380	1.00[CHB][hapmap];0.84[JPT][hapmap];0.89[ASN][1000 genomes]
rs640845	0.87[CHB][hapmap];0.89[ASN][1000 genomes]
rs644722	0.83[CHB][hapmap];0.83[JPT][hapmap];0.84[ASN][1000 genomes]
rs644748	0.82[CHB][hapmap];0.83[JPT][hapmap];0.84[ASN][1000 genomes]
rs685008	0.83[ASN][1000 genomes]
rs7742242	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs9356949	0.89[ASN][1000 genomes]
rs9379698	0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	nsv1019504	chr6:24869174-24994758	Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Genic enhancers Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	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
5	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

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:24920600-24932000	Weak transcription	Fetal Kidney	kidney
2	chr6:24925600-24931800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr6:24926800-24931600	Weak transcription	Stomach Mucosa	stomach
4	chr6:24926800-24934400	Transcr. at gene 5' and 3'	Primary B cells from cord blood	blood
5	chr6:24927000-24931600	Weak transcription	Fetal Intestine Small	intestine
6	chr6:24927200-24933600	Transcr. at gene 5' and 3'	Primary T cells fromperipheralblood	blood
7	chr6:24927400-24931800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
8	chr6:24927400-24932200	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
9	chr6:24927600-24931600	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr6:24927600-24932400	Transcr. at gene 5' and 3'	Primary T killer memory cells from peripheral blood	blood
11	chr6:24927800-24931400	Enhancers	Osteobl	bone
12	chr6:24927800-24932800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr6:24927800-24933200	Enhancers	HSMM	muscle
14	chr6:24927800-24934400	Enhancers	HSMMtube	muscle
15	chr6:24928000-24931600	Genic enhancers	Primary monocytes fromperipheralblood	blood
16	chr6:24928000-24933400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr6:24928000-24934200	Enhancers	Fetal Lung	lung
18	chr6:24928200-24931800	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
19	chr6:24928200-24933000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr6:24928400-24932600	Enhancers	Cortex derived primary cultured neurospheres	brain
21	chr6:24928400-24933000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr6:24928400-24933400	Enhancers	Fetal Heart	heart
23	chr6:24928800-24933400	Transcr. at gene 5' and 3'	Primary T regulatory cells fromperipheralblood	blood
24	chr6:24929000-24932600	Flanking Active TSS	GM12878-XiMat	blood
25	chr6:24929000-24935200	Transcr. at gene 5' and 3'	Primary B cells from peripheral blood	blood
26	chr6:24929200-24931200	Enhancers	NHLF	lung
27	chr6:24929200-24932000	Weak transcription	Rectal Mucosa Donor 29	rectum
28	chr6:24929200-24932400	Transcr. at gene 5' and 3'	Primary T cells from cord blood	blood
29	chr6:24929200-24932400	Transcr. at gene 5' and 3'	Primary T helper naive cells from peripheral blood	blood
30	chr6:24929400-24932200	Enhancers	Adipose Nuclei	Adipose
31	chr6:24929400-24932400	Transcr. at gene 5' and 3'	Primary mononuclear cells fromperipheralblood	Blood
32	chr6:24929400-24932400	Enhancers	Fetal Muscle Leg	muscle
33	chr6:24929400-24932400	Enhancers	Fetal Stomach	stomach
34	chr6:24929400-24932600	Transcr. at gene 5' and 3'	Monocytes-CD14+_RO01746	blood
35	chr6:24929400-24933000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr6:24929400-24934200	Transcr. at gene 5' and 3'	Primary neutrophils fromperipheralblood	blood
37	chr6:24929600-24931200	Transcr. at gene 5' and 3'	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr6:24929600-24932200	Transcr. at gene 5' and 3'	Primary T helper naive cells fromperipheralblood	blood
39	chr6:24929600-24932200	Enhancers	Psoas Muscle	Psoas
40	chr6:24929600-24932400	Enhancers	Skeletal Muscle Male	skeletal muscle
41	chr6:24929600-24932800	Enhancers	Skeletal Muscle Female	skeletal muscle
42	chr6:24929600-24936000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr6:24929800-24931600	Weak transcription	Thymus	Thymus
44	chr6:24929800-24932400	Transcr. at gene 5' and 3'	Primary T helper cells fromperipheralblood	blood
45	chr6:24929800-24932800	Enhancers	NHDF-Ad	bronchial
46	chr6:24930000-24931600	Enhancers	Dnd41	blood
47	chr6:24930000-24932200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr6:24930200-24931600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr6:24930200-24932800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr6:24930200-24933000	Enhancers	Colon Smooth Muscle	Colon

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