Variant report

Variant	rs12062672
Chromosome Location	chr1:241672586-241672587
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	chr1:241671168..241675196-chr1:241680746..241684260,5	MCF-7	breast:
2	chr1:241665859..241668124-chr1:241670823..241673465,2	K562	blood:

Variant related genes	Relation type
ENSG00000091483	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10802967	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10926503	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10926511	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12059375	0.91[AFR][1000 genomes]
rs12059383	1.00[ASW][hapmap];0.81[LWK][hapmap];0.85[YRI][hapmap];0.91[AFR][1000 genomes]
rs12065955	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12072983	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2105079	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2341939	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3765801	1.00[CHB][hapmap];0.92[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4660070	1.00[TSI][hapmap]
rs4660098	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4660102	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs57644653	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7540071	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	nsv918034	chr1:241072791-242005532	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	32 gene(s)	inside rSNPs	diseases
2	nsv997966	chr1:241100739-242087629	Active TSS Genic enhancers Flanking Active TSS Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	40 gene(s)	inside rSNPs	diseases
3	nsv949442	chr1:241432051-241730054	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv1002214	chr1:241458939-242099790	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
5	nsv549460	chr1:241494578-241833287	Genic enhancers Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
6	nsv1009579	chr1:241499537-241824631	Bivalent/Poised TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
7	nsv530112	chr1:241522031-241840269	Strong transcription Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
8	nsv873368	chr1:241533392-242195928	Weak transcription Active TSS Transcr. at gene 5' and 3' Enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
9	nsv873371	chr1:241667244-241747838	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:241655800-241677200	Strong transcription	Liver	Liver
2	chr1:241656800-241677000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr1:241656800-241678200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr1:241657000-241675800	Strong transcription	Stomach Smooth Muscle	stomach
5	chr1:241657000-241676000	Strong transcription	Rectal Mucosa Donor 29	rectum
6	chr1:241657000-241676200	Strong transcription	Duodenum Smooth Muscle	Duodenum
7	chr1:241657000-241676400	Strong transcription	Primary T helper cells fromperipheralblood	blood
8	chr1:241657000-241677000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
9	chr1:241657000-241677200	Strong transcription	Adipose Nuclei	Adipose
10	chr1:241657000-241677400	Strong transcription	Fetal Thymus	thymus
11	chr1:241657000-241680000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr1:241657200-241677000	Strong transcription	Primary T cells fromperipheralblood	blood
13	chr1:241657200-241677200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr1:241657200-241677400	Strong transcription	Duodenum Mucosa	Duodenum
15	chr1:241657400-241676600	Strong transcription	Primary B cells from peripheral blood	blood
16	chr1:241657400-241676800	Strong transcription	K562	blood
17	chr1:241657400-241678600	Strong transcription	Dnd41	blood
18	chr1:241657400-241680000	Strong transcription	Primary B cells from cord blood	blood
19	chr1:241657600-241676600	Strong transcription	Placenta	Placenta
20	chr1:241657600-241677000	Strong transcription	Primary T helper cells PMA-I stimulated	--
21	chr1:241659000-241682000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr1:241659200-241679800	Strong transcription	HUES64 Cell Line	embryonic stem cell
23	chr1:241659600-241679000	Strong transcription	HMEC	breast
24	chr1:241660000-241675800	Strong transcription	Primary neutrophils fromperipheralblood	blood
25	chr1:241661200-241681400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr1:241662800-241676000	Strong transcription	Skeletal Muscle Male	skeletal muscle
27	chr1:241663000-241675200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr1:241663800-241675800	Strong transcription	Left Ventricle	heart
29	chr1:241663800-241676000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
30	chr1:241663800-241676000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr1:241663800-241677000	Strong transcription	Fetal Muscle Trunk	muscle
32	chr1:241664000-241676800	Strong transcription	GM12878-XiMat	blood
33	chr1:241664000-241677200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr1:241664400-241677000	Strong transcription	Skeletal Muscle Female	skeletal muscle
35	chr1:241664800-241675400	Strong transcription	Ovary	ovary
36	chr1:241664800-241675800	Strong transcription	Fetal Muscle Leg	muscle
37	chr1:241664800-241676600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr1:241664800-241677000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr1:241664800-241680600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr1:241665000-241672800	Strong transcription	H1 Cell Line	embryonic stem cell
41	chr1:241665000-241674800	Strong transcription	Small Intestine	intestine
42	chr1:241665000-241676400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr1:241665000-241676400	Strong transcription	Brain Anterior Caudate	brain
44	chr1:241665000-241677000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr1:241665000-241677000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr1:241665000-241677400	Strong transcription	HUES48 Cell Line	embryonic stem cell
47	chr1:241665000-241677400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
48	chr1:241665000-241679200	Strong transcription	Hela-S3	cervix
49	chr1:241665000-241679600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr1:241665200-241676000	Strong transcription	Brain Inferior Temporal Lobe	brain

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