Variant report

Variant	rs28694585
Chromosome Location	chr2:47192963-47192964
allele	A/G
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:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:47192520..47194152-chr2:47197519..47201107,3	K562	blood:
2	chr2:47164600..47167090-chr2:47190950..47193614,2	K562	blood:
3	chr2:47192215..47193859-chr2:47323314..47325455,2	MCF-7	breast:
4	chr2:47192694..47195211-chr2:47401865..47404549,2	MCF-7	breast:
5	chr2:47187408..47189376-chr2:47192162..47193765,2	K562	blood:
6	chr2:47187193..47190243-chr2:47190337..47193752,4	MCF-7	breast:
7	chr2:47166769..47171325-chr2:47189456..47193821,11	MCF-7	breast:
8	chr2:47191916..47197742-chr2:47401234..47405560,7	MCF-7	breast:
9	chr2:47164675..47170526-chr2:47188235..47196918,12	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000068724	Chromatin interaction
ENSG00000180398	Chromatin interaction
ENSG00000143933	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10495941	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11125103	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11125104	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11125105	0.86[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs1122516	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11680492	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11685461	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12053441	0.82[EUR][1000 genomes]
rs12712980	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12712981	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12712982	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12712984	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13014374	0.90[ASN][1000 genomes]
rs1865261	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2278449	0.93[EUR][1000 genomes]
rs2278450	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28434195	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4952857	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4953437	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4953438	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6544943	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6544944	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6713810	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6727651	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6745836	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs735887	0.89[ASN][1000 genomes]
rs735888	0.89[ASN][1000 genomes]
rs7557193	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7602813	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs892380	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817517	chr2:46819371-47715140	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
2	nsv457352	chr2:47004788-47325973	Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv581749	chr2:47004788-47325973	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	nsv1004828	chr2:47056849-47814482	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
5	nsv524970	chr2:47162739-47302095	Enhancers Genic enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
6	nsv1000377	chr2:47189386-47344029	Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:47169800-47214600	Weak transcription	Fetal Kidney	kidney
2	chr2:47174400-47212400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr2:47177200-47210400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr2:47179200-47195000	Strong transcription	Fetal Thymus	thymus
5	chr2:47179400-47193800	Strong transcription	Primary B cells from peripheral blood	blood
6	chr2:47181600-47210800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr2:47183000-47195000	Weak transcription	Small Intestine	intestine
8	chr2:47183400-47193400	Strong transcription	Fetal Intestine Small	intestine
9	chr2:47184200-47194400	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr2:47184600-47197600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr2:47184600-47205000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr2:47185000-47206000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr2:47185200-47210200	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr2:47185400-47205800	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr2:47185400-47210400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr2:47185600-47195000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
17	chr2:47185800-47195000	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr2:47186000-47194400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr2:47186000-47195000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr2:47186000-47195000	Weak transcription	Left Ventricle	heart
21	chr2:47186200-47200800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr2:47186400-47205600	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr2:47186600-47194400	Weak transcription	Colon Smooth Muscle	Colon
24	chr2:47186800-47205200	Weak transcription	Gastric	stomach
25	chr2:47186800-47205800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
26	chr2:47187000-47195000	Weak transcription	Right Ventricle	heart
27	chr2:47187200-47197000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr2:47187400-47206000	Weak transcription	Fetal Brain Female	brain
29	chr2:47187600-47194600	Weak transcription	Rectal Smooth Muscle	rectum
30	chr2:47187800-47194800	Weak transcription	HUES6 Cell Line	embryonic stem cell
31	chr2:47187800-47195000	Weak transcription	Colonic Mucosa	Colon
32	chr2:47187800-47203200	Weak transcription	Brain Germinal Matrix	brain
33	chr2:47187800-47210200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
34	chr2:47188000-47194400	Weak transcription	Duodenum Smooth Muscle	Duodenum
35	chr2:47188000-47194400	Weak transcription	Fetal Lung	lung
36	chr2:47188000-47205200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
37	chr2:47188000-47207000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr2:47188200-47196800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
39	chr2:47189000-47193600	Enhancers	Breast Myoepithelial Primary Cells	Breast
40	chr2:47189800-47194400	Weak transcription	Duodenum Mucosa	Duodenum
41	chr2:47189800-47195000	Weak transcription	Primary T helper cells PMA-I stimulated	--
42	chr2:47189800-47195000	Weak transcription	Fetal Muscle Leg	muscle
43	chr2:47190000-47193000	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr2:47190000-47194800	Weak transcription	Primary T cells fromperipheralblood	blood
45	chr2:47190000-47195000	Weak transcription	Right Atrium	heart
46	chr2:47190000-47197000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr2:47190200-47193000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr2:47190200-47193600	Enhancers	HMEC	breast
49	chr2:47190200-47194400	Weak transcription	Primary neutrophils fromperipheralblood	blood
50	chr2:47190200-47194400	Weak transcription	Primary T helper cells fromperipheralblood	blood

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