Variant report

Variant	rs3129583
Chromosome Location	chr1:246748477-246748478
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:246730131..246732589-chr1:246747162..246749763,2	MCF-7	breast:
2	chr1:246746217..246748591-chr1:246759216..246761418,2	K562	blood:

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10754528	1.00[ASN][1000 genomes]
rs10754530	0.95[ASN][1000 genomes]
rs10924785	0.95[ASN][1000 genomes]
rs3006082	0.99[ASN][1000 genomes]
rs3006085	0.95[ASN][1000 genomes]
rs3007401	0.99[ASN][1000 genomes]
rs3007405	0.89[ASN][1000 genomes]
rs3007406	0.95[ASN][1000 genomes]
rs3124075	0.94[ASN][1000 genomes]
rs3124077	0.89[ASN][1000 genomes]
rs3124078	0.89[ASN][1000 genomes]
rs3124079	0.87[ASN][1000 genomes]
rs3124084	0.85[ASN][1000 genomes]
rs3129542	0.85[ASN][1000 genomes]
rs3129544	0.89[ASN][1000 genomes]
rs3129546	0.89[ASN][1000 genomes]
rs3129547	0.89[ASN][1000 genomes]
rs3129552	0.95[ASN][1000 genomes]
rs3129557	0.81[ASN][1000 genomes]
rs4654122	0.95[ASN][1000 genomes]
rs4654123	0.84[ASN][1000 genomes]
rs72762785	0.94[ASN][1000 genomes]
rs7520403	0.95[ASN][1000 genomes]
rs7539592	0.95[ASN][1000 genomes]
rs9426203	0.89[ASN][1000 genomes]
rs9426250	0.89[ASN][1000 genomes]
rs9426251	0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:25 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1004119	chr1:245957145-246813150	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
2	nsv535389	chr1:245957145-246813150	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
3	nsv1014529	chr1:245957145-246817877	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
4	nsv1000654	chr1:245966390-246778182	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
5	nsv535392	chr1:245966390-246778182	Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
6	nsv868852	chr1:245969229-246811220	Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
7	nsv948348	chr1:246090818-246853200	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
8	nsv430402	chr1:246124959-246787448	Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
9	nsv497890	chr1:246143172-246778453	Enhancers Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
10	nsv1013800	chr1:246472691-246840960	Strong transcription Flanking Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
11	nsv535409	chr1:246472691-246840960	Flanking Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
12	esv2762191	chr1:246546436-246815064	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
13	nsv1002805	chr1:246608164-246890518	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
14	nsv535413	chr1:246608164-246890518	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
15	nsv1010453	chr1:246645797-246815052	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
16	nsv998579	chr1:246666041-246817877	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
17	nsv1010316	chr1:246686301-246840960	Strong transcription Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
18	nsv535414	chr1:246686301-246840960	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
19	nsv949571	chr1:246688635-247240863	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
20	nsv873420	chr1:246706139-246755124	Enhancers Active TSS Strong transcription Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
21	nsv528615	chr1:246708467-246843315	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS 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	17 gene(s)	inside rSNPs	diseases
22	nsv1014280	chr1:246709243-246823255	Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
23	nsv1013264	chr1:246723012-246807400	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
24	nsv535415	chr1:246723012-246807400	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
25	nsv1005214	chr1:246730885-246841107	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:246731400-246753400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr1:246735600-246754800	Weak transcription	Spleen	Spleen
3	chr1:246738000-246753400	Weak transcription	Primary neutrophils fromperipheralblood	blood
4	chr1:246739000-246806200	Weak transcription	Aorta	Aorta
5	chr1:246741200-246750400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr1:246741200-246751000	Weak transcription	HSMMtube	muscle
7	chr1:246742200-246765600	Weak transcription	HSMM	muscle
8	chr1:246742600-246750600	Weak transcription	NH-A	brain
9	chr1:246743000-246753400	Weak transcription	Placenta	Placenta
10	chr1:246743600-246748800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr1:246744000-246749400	Enhancers	Ovary	ovary
12	chr1:246744000-246754800	Weak transcription	Fetal Brain Female	brain
13	chr1:246744400-246758600	Weak transcription	Fetal Brain Male	brain
14	chr1:246744400-246770800	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr1:246744600-246749000	Enhancers	Small Intestine	intestine
16	chr1:246744800-246748800	Genic enhancers	Primary T helper cells PMA-I stimulated	--
17	chr1:246744800-246753400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr1:246745400-246748800	Genic enhancers	Primary T helper cells fromperipheralblood	blood
19	chr1:246745400-246748800	Strong transcription	Thymus	Thymus
20	chr1:246745600-246748600	Enhancers	Left Ventricle	heart
21	chr1:246745600-246748800	Strong transcription	Fetal Thymus	thymus
22	chr1:246745800-246748600	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
23	chr1:246745800-246749600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
24	chr1:246745800-246755200	Weak transcription	HUES64 Cell Line	embryonic stem cell
25	chr1:246746000-246748800	Strong transcription	Primary B cells from peripheral blood	blood
26	chr1:246746000-246748800	Genic enhancers	Fetal Stomach	stomach
27	chr1:246746000-246749200	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr1:246746200-246748600	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr1:246746200-246748600	Enhancers	Brain Hippocampus Middle	brain
30	chr1:246746200-246748800	Enhancers	Brain Substantia Nigra	brain
31	chr1:246746200-246749000	Enhancers	Fetal Muscle Leg	muscle
32	chr1:246746200-246749200	Enhancers	Skeletal Muscle Female	skeletal muscle
33	chr1:246746400-246748800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr1:246746400-246748800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr1:246746400-246754800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr1:246746400-246755000	Weak transcription	Lung	lung
37	chr1:246746600-246748600	Enhancers	Duodenum Smooth Muscle	Duodenum
38	chr1:246746800-246748600	Strong transcription	Primary T cells from cord blood	blood
39	chr1:246746800-246748600	Enhancers	Brain Inferior Temporal Lobe	brain
40	chr1:246747000-246748600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
41	chr1:246747000-246748600	Flanking Active TSS	Liver	Liver
42	chr1:246747000-246748600	Enhancers	Right Ventricle	heart
43	chr1:246747000-246749000	Enhancers	Right Atrium	heart
44	chr1:246747000-246749200	Enhancers	Pancreas	Pancrea
45	chr1:246747000-246749400	Enhancers	Psoas Muscle	Psoas
46	chr1:246747000-246753400	Weak transcription	Cortex derived primary cultured neurospheres	brain
47	chr1:246747000-246761000	Weak transcription	Fetal Heart	heart
48	chr1:246747200-246748600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr1:246747200-246748600	Enhancers	Gastric	stomach
50	chr1:246747200-246748600	Genic enhancers	Sigmoid Colon	Sigmoid Colon

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