Variant report

Variant	rs4560164
Chromosome Location	chr2:47536547-47536548
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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:47398263..47400819-chr2:47535902..47539310,3	MCF-7	breast:
2	chr2:47529997..47532403-chr2:47536425..47538382,2	K562	blood:
3	chr2:47402318..47405024-chr2:47536306..47539127,3	MCF-7	breast:
4	chr2:47395267..47408439-chr2:47533772..47553038,55	MCF-7	breast:
5	chr2:47398936..47406040-chr2:47522760..47537371,25	K562	blood:
6	chr2:47536098..47538713-chr2:47547950..47550505,2	MCF-7	breast:
7	chr2:47500714..47503481-chr2:47536098..47539031,2	K562	blood:
8	chr2:47402139..47404719-chr2:47535417..47537672,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000143933	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10180711	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12471906	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4558636	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6544977	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6544978	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6720211	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9789479	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9789683	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[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	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
3	nsv531348	chr2:47433147-47827310	Flanking Bivalent TSS/Enh Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
4	nsv457385	chr2:47468331-47552277	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv581755	chr2:47468331-47552277	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Strong transcription	Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv999576	chr2:47506116-47773960	Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers 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 miRNA target site	43 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:47519800-47537200	Weak transcription	Fetal Stomach	stomach
2	chr2:47520800-47540000	Enhancers	Primary monocytes fromperipheralblood	blood
3	chr2:47523200-47537000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr2:47523400-47536600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr2:47523600-47536800	Weak transcription	Fetal Kidney	kidney
6	chr2:47525400-47537400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr2:47526400-47536800	Weak transcription	Fetal Lung	lung
8	chr2:47526400-47536800	Weak transcription	Spleen	Spleen
9	chr2:47526600-47537800	Weak transcription	Fetal Brain Male	brain
10	chr2:47527400-47536800	Weak transcription	Brain Germinal Matrix	brain
11	chr2:47528600-47536800	Weak transcription	Psoas Muscle	Psoas
12	chr2:47529200-47536800	Enhancers	Brain Substantia Nigra	brain
13	chr2:47529400-47538000	Weak transcription	Small Intestine	intestine
14	chr2:47530400-47536800	Enhancers	Brain Inferior Temporal Lobe	brain
15	chr2:47530400-47541200	Enhancers	Fetal Intestine Small	intestine
16	chr2:47530400-47541600	Enhancers	Fetal Intestine Large	intestine
17	chr2:47531000-47536800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr2:47531000-47537000	Weak transcription	Osteobl	bone
19	chr2:47531200-47536600	Weak transcription	Primary hematopoietic stem cells	blood
20	chr2:47531200-47536800	Weak transcription	HUES6 Cell Line	embryonic stem cell
21	chr2:47531200-47536800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr2:47532000-47537200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr2:47532200-47537400	Weak transcription	HSMM	muscle
24	chr2:47532400-47536800	Enhancers	Brain Anterior Caudate	brain
25	chr2:47532600-47536800	Enhancers	Monocytes-CD14+_RO01746	blood
26	chr2:47533800-47536600	Enhancers	Duodenum Mucosa	Duodenum
27	chr2:47534200-47536800	Enhancers	Primary neutrophils fromperipheralblood	blood
28	chr2:47534400-47536800	Weak transcription	Adipose Nuclei	Adipose
29	chr2:47534400-47537400	Enhancers	Primary hematopoietic stem cells short term culture	blood
30	chr2:47534400-47550400	Weak transcription	Ovary	ovary
31	chr2:47534600-47536600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr2:47534600-47537000	Weak transcription	NHLF	lung
33	chr2:47534600-47537800	Weak transcription	Fetal Brain Female	brain
34	chr2:47534800-47536600	Weak transcription	Cortex derived primary cultured neurospheres	brain
35	chr2:47534800-47536800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr2:47534800-47536800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr2:47534800-47536800	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr2:47534800-47536800	Weak transcription	Fetal Heart	heart
39	chr2:47535000-47536800	Enhancers	GM12878-XiMat	blood
40	chr2:47535000-47538800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr2:47535000-47540600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr2:47535400-47536600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr2:47535400-47536600	Weak transcription	Placenta	Placenta
44	chr2:47535400-47537000	Weak transcription	Colon Smooth Muscle	Colon
45	chr2:47535800-47536800	Weak transcription	HUES64 Cell Line	embryonic stem cell
46	chr2:47535800-47536800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr2:47536000-47536800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr2:47536200-47536600	Enhancers	A549	lung
49	chr2:47536200-47536800	Enhancers	Brain Cingulate Gyrus	brain
50	chr2:47536200-47537000	Enhancers	Lung	lung

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