Variant report

Variant	rs2328874
Chromosome Location	chr6:25223827-25223828
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:25217783..25220608-chr6:25221388..25225373,4	K562	blood:
2	chr6:25223432..25224370-chr6:25602035..25603142,3	K562	blood:
3	chr6:25223391..25224244-chr6:25556059..25557190,5	MCF-7	breast:
4	chr6:25223464..25224040-chr6:25602333..25602833,2	MCF-7	breast:
5	chr6:25223441..25224407-chr6:25489990..25490901,3	MCF-7	breast:
6	chr6:25223112..25223956-chr6:25556335..25557349,3	K562	blood:
7	chr6:25223414..25224084-chr6:25490024..25490742,2	K562	blood:
8	chr6:25216145..25218420-chr6:25221724..25223858,2	MCF-7	breast:
9	chr6:25223636..25224166-chr6:25265963..25266626,2	MCF-7	breast:
10	chr6:25223811..25224359-chr6:25489995..25490562,2	MCF-7	breast:
11	chr6:25218882..25222296-chr6:25222360..25226467,5	K562	blood:

No data

Variant related genes	Relation type
ENSG00000219681	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs1880269	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2328875	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4443502	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4712895	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4712898	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61563072	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6908491	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6939574	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	nsv1025694	chr6:25136860-25309450	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
3	nsv1020774	chr6:25154152-25285679	Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv538161	chr6:25154152-25285679	Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	nsv462663	chr6:25156197-25234884	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv601167	chr6:25156197-25234884	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	nsv883483	chr6:25200842-25272435	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25218200-25224000	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr6:25218800-25224000	Weak transcription	Fetal Thymus	thymus
3	chr6:25219600-25224000	Weak transcription	Fetal Muscle Leg	muscle
4	chr6:25219600-25224200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr6:25220400-25224000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr6:25221400-25224000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr6:25221400-25229200	Weak transcription	Placenta	Placenta
8	chr6:25221400-25229400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr6:25222000-25224400	Enhancers	Hela-S3	cervix
10	chr6:25222400-25226200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
11	chr6:25222600-25224200	Enhancers	HSMM	muscle
12	chr6:25222800-25224000	Enhancers	Fetal Kidney	kidney
13	chr6:25222800-25224000	Weak transcription	NH-A	brain
14	chr6:25222800-25224600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr6:25222800-25225400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr6:25223000-25224000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
17	chr6:25223200-25224000	Enhancers	HMEC	breast
18	chr6:25223400-25224000	Enhancers	Adipose Nuclei	Adipose
19	chr6:25223400-25224200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr6:25223400-25224400	Enhancers	Primary monocytes fromperipheralblood	blood
21	chr6:25223400-25224800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr6:25223600-25224000	Enhancers	Muscle Satellite Cultured Cells	--
23	chr6:25223600-25224000	Enhancers	Skeletal Muscle Male	skeletal muscle
24	chr6:25223600-25224200	Enhancers	iPS-15b Cell Line	embryonic stem cell
25	chr6:25223600-25224200	Enhancers	Primary B cells from peripheral blood	blood
26	chr6:25223600-25224200	Enhancers	Fetal Brain Female	brain
27	chr6:25223600-25224200	Enhancers	Fetal Intestine Large	intestine
28	chr6:25223600-25224200	Enhancers	Rectal Mucosa Donor 31	rectum
29	chr6:25223600-25224400	Enhancers	Primary hematopoietic stem cells	blood
30	chr6:25223600-25224400	Enhancers	Brain Cingulate Gyrus	brain
31	chr6:25223600-25224400	Enhancers	Stomach Mucosa	stomach
32	chr6:25223600-25224400	Enhancers	NHEK	skin
33	chr6:25223800-25224000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr6:25223800-25224000	Active TSS	Primary T cells from cord blood	blood
35	chr6:25223800-25224000	Active TSS	Primary T cells fromperipheralblood	blood
36	chr6:25223800-25224000	Active TSS	Primary T helper naive cells from peripheral blood	blood
37	chr6:25223800-25224000	Active TSS	Primary T regulatory cells fromperipheralblood	blood
38	chr6:25223800-25224000	Active TSS	Primary T killer naive cells fromperipheralblood	blood
39	chr6:25223800-25224000	Active TSS	Cortex derived primary cultured neurospheres	brain
40	chr6:25223800-25224000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr6:25223800-25224000	Active TSS	Brain Hippocampus Middle	brain
42	chr6:25223800-25224000	Active TSS	Duodenum Smooth Muscle	Duodenum
43	chr6:25223800-25224000	Active TSS	Rectal Mucosa Donor 29	rectum
44	chr6:25223800-25224000	Active TSS	Thymus	Thymus
45	chr6:25223800-25224000	Active TSS	HUVEC	blood vessel
46	chr6:25223800-25224000	Active TSS	NHLF	lung
47	chr6:25223800-25224200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr6:25223800-25224200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr6:25223800-25224200	Active TSS	Breast Myoepithelial Primary Cells	Breast
50	chr6:25223800-25224200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--

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