Variant report

Variant	rs28556964
Chromosome Location	chr2:47314095-47314096
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:47312417..47315295-chr2:47318337..47320421,2	MCF-7	breast:
2	chr2:47312009..47319415-chr2:47398595..47405362,13	K562	blood:
3	chr2:47308385..47311551-chr2:47313858..47316379,4	MCF-7	breast:
4	chr2:47311949..47314446-chr2:47401904..47404430,2	K562	blood:
5	chr2:47303169..47307562-chr2:47312603..47317235,6	MCF-7	breast:
6	chr2:47292470..47294231-chr2:47312164..47314753,2	K562	blood:
7	chr2:47313243..47315794-chr2:47321683..47323508,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000143933	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs13411522	1.00[ASW][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.86[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13417534	0.82[ASW][hapmap]
rs73926707	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs919878	1.00[MEX][hapmap]
rs924229	1.00[MEX][hapmap]

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	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	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
6	nsv2716	chr2:47312166-47336600	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv457374	chr2:47313624-47448865	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	87 gene(s)	inside rSNPs	diseases
8	nsv581754	chr2:47313624-47448865	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	87 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:47307200-47315800	Weak transcription	HUES64 Cell Line	embryonic stem cell
2	chr2:47307200-47323000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr2:47307400-47316200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr2:47307600-47315400	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr2:47307600-47315600	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr2:47307600-47316000	Weak transcription	NHDF-Ad	bronchial
7	chr2:47309800-47317800	Enhancers	Fetal Muscle Trunk	muscle
8	chr2:47310000-47316600	Enhancers	Skeletal Muscle Male	skeletal muscle
9	chr2:47310000-47318600	Enhancers	Fetal Muscle Leg	muscle
10	chr2:47310200-47317200	Enhancers	Left Ventricle	heart
11	chr2:47310400-47314600	Enhancers	Brain Substantia Nigra	brain
12	chr2:47310400-47315600	Enhancers	Duodenum Mucosa	Duodenum
13	chr2:47310400-47318800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr2:47310600-47314800	Enhancers	Stomach Mucosa	stomach
15	chr2:47310600-47317400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
16	chr2:47310800-47319200	Enhancers	Fetal Lung	lung
17	chr2:47310800-47319200	Enhancers	HUVEC	blood vessel
18	chr2:47311200-47316000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr2:47311200-47317200	Enhancers	Spleen	Spleen
20	chr2:47311400-47318600	Weak transcription	Liver	Liver
21	chr2:47311600-47315600	Weak transcription	Gastric	stomach
22	chr2:47311600-47317000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr2:47311800-47314600	Enhancers	Breast Myoepithelial Primary Cells	Breast
24	chr2:47311800-47316600	Enhancers	Skeletal Muscle Female	skeletal muscle
25	chr2:47312200-47314200	Enhancers	Brain Hippocampus Middle	brain
26	chr2:47312200-47314200	Enhancers	K562	blood
27	chr2:47312200-47314400	Enhancers	Fetal Stomach	stomach
28	chr2:47312200-47314600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr2:47312200-47314600	Enhancers	Brain Cingulate Gyrus	brain
30	chr2:47312200-47314800	Enhancers	Psoas Muscle	Psoas
31	chr2:47312400-47314400	Enhancers	Cortex derived primary cultured neurospheres	brain
32	chr2:47312400-47314400	Enhancers	Fetal Kidney	kidney
33	chr2:47312400-47314400	Enhancers	NHLF	lung
34	chr2:47312400-47314600	Enhancers	Small Intestine	intestine
35	chr2:47312400-47314800	Enhancers	A549	lung
36	chr2:47312600-47314400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr2:47312600-47314600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr2:47312600-47314600	Enhancers	Right Atrium	heart
39	chr2:47312600-47314800	Enhancers	Colon Smooth Muscle	Colon
40	chr2:47312600-47316600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr2:47312800-47314400	Enhancers	Brain Anterior Caudate	brain
42	chr2:47312800-47316600	Enhancers	Right Ventricle	heart
43	chr2:47313000-47314400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr2:47313000-47314400	Enhancers	Brain Inferior Temporal Lobe	brain
45	chr2:47313000-47314400	Enhancers	Esophagus	oesophagus
46	chr2:47313000-47314400	Enhancers	HMEC	breast
47	chr2:47313000-47314600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr2:47313000-47314800	Enhancers	Ovary	ovary
49	chr2:47313000-47317200	Enhancers	Fetal Intestine Small	intestine
50	chr2:47313000-47317800	Enhancers	Lung	lung

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