Variant report

Variant	rs2493415
Chromosome Location	chr1:120492200-120492201
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:120489170..120492877-chr1:120510169..120513121,3	K562	blood:
2	chr1:120491579..120494210-chr1:120499426..120502026,2	MCF-7	breast:
3	chr1:120491383..120493065-chr1:120495646..120497654,2	MCF-7	breast:

Extended variants
information (count: 39 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10127888	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10923931	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1493694	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1738647	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2027447	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2453040	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2453058	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2493389	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2493390	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2493391	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2493392	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2493394	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2493413	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2641317	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2641348	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2641352	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2793829	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2793831	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2934381	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2934387	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3897478	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56302051	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6668119	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6685892	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs699779	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72697237	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7515431	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7534585	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7534586	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs835575	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs835576	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv428201	chr1:120267313-120697156	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	esv2757750	chr1:120267313-121226013	Enhancers Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
3	esv2758965	chr1:120267313-121226013	Enhancers Bivalent/Poised TSS Bivalent Enhancer Weak transcription Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
4	esv1816057	chr1:120469050-120697156	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
5	esv1818054	chr1:120469050-120697156	Enhancers Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
6	esv1844863	chr1:120469050-120697156	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
7	esv1850218	chr1:120469050-120697156	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
8	nsv427730	chr1:120469050-120697156	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 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	chr1:120468400-120495800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr1:120468400-120506200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr1:120468400-120507400	Weak transcription	Right Ventricle	heart
4	chr1:120468600-120496000	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr1:120468600-120532800	Weak transcription	Stomach Mucosa	stomach
6	chr1:120476400-120507400	Weak transcription	Brain Angular Gyrus	brain
7	chr1:120477000-120497200	Weak transcription	Small Intestine	intestine
8	chr1:120478800-120508800	Weak transcription	A549	lung
9	chr1:120478800-120511000	Strong transcription	Monocytes-CD14+_RO01746	blood
10	chr1:120479000-120511000	Strong transcription	Primary monocytes fromperipheralblood	blood
11	chr1:120479600-120493000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr1:120479600-120504000	Weak transcription	Brain Cingulate Gyrus	brain
13	chr1:120480400-120507800	Weak transcription	Fetal Brain Female	brain
14	chr1:120480600-120492400	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr1:120480600-120492600	Weak transcription	HUVEC	blood vessel
16	chr1:120480600-120495000	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr1:120480600-120503600	Weak transcription	Brain Substantia Nigra	brain
18	chr1:120480600-120507400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr1:120483400-120492600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr1:120483600-120492400	Weak transcription	Brain Hippocampus Middle	brain
21	chr1:120483600-120496000	Weak transcription	Brain Anterior Caudate	brain
22	chr1:120484000-120492800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
23	chr1:120484200-120492400	Weak transcription	Psoas Muscle	Psoas
24	chr1:120484400-120495400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr1:120484400-120506000	Weak transcription	Gastric	stomach
26	chr1:120484600-120505800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr1:120488800-120510400	Strong transcription	Primary B cells from peripheral blood	blood
28	chr1:120489200-120499000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr1:120489600-120492400	Weak transcription	Colon Smooth Muscle	Colon
30	chr1:120490000-120498000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr1:120490000-120498000	Strong transcription	HUES64 Cell Line	embryonic stem cell
32	chr1:120490000-120499000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr1:120490000-120500000	Strong transcription	Duodenum Smooth Muscle	Duodenum
34	chr1:120490000-120512400	Strong transcription	Primary T cells fromperipheralblood	blood
35	chr1:120490000-120514400	Strong transcription	Primary neutrophils fromperipheralblood	blood
36	chr1:120490000-120517600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr1:120490200-120494200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
38	chr1:120490200-120494200	Strong transcription	Liver	Liver
39	chr1:120490200-120494400	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
40	chr1:120490200-120496800	Strong transcription	Fetal Kidney	kidney
41	chr1:120490200-120498000	Strong transcription	Primary hematopoietic stem cells	blood
42	chr1:120490200-120498000	Strong transcription	Placenta	Placenta
43	chr1:120490200-120498000	Strong transcription	Rectal Mucosa Donor 31	rectum
44	chr1:120490200-120498000	Strong transcription	Dnd41	blood
45	chr1:120490200-120498200	Strong transcription	Rectal Mucosa Donor 29	rectum
46	chr1:120490200-120512600	Strong transcription	Primary T cells from cord blood	blood
47	chr1:120490200-120512600	Strong transcription	Primary T helper cells fromperipheralblood	blood
48	chr1:120490200-120521000	Strong transcription	Primary B cells from cord blood	blood
49	chr1:120490400-120497800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr1:120490400-120498000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood

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