Variant report

Variant	rs2972091
Chromosome Location	chr2:55339203-55339204
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:54341515..54343973-chr2:55337394..55340042,2	MCF-7	breast:
2	chr2:55273237..55280299-chr2:55335301..55344768,18	K562	blood:
3	chr2:55273237..55279836-chr2:55336432..55344363,17	K562	blood:

Variant related genes	Relation type
ENSG00000115310	Chromatin interaction
ENSG00000170634	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs2920843	0.83[AMR][1000 genomes]
rs2920872	0.83[EUR][1000 genomes]
rs2968807	0.83[EUR][1000 genomes]
rs2968810	0.83[EUR][1000 genomes]
rs2968812	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2968813	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2968814	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2968816	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2968820	0.94[EUR][1000 genomes]
rs2972084	0.83[EUR][1000 genomes]
rs2972085	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2972087	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1006172	chr2:55322883-55340812	Weak transcription Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv999212	chr2:55324276-55340812	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv1004503	chr2:55324276-55343705	Enhancers Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv997458	chr2:55324276-55344326	Enhancers Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv1013316	chr2:55324276-55345262	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55321600-55339400	Weak transcription	Thymus	Thymus
2	chr2:55325200-55340400	Weak transcription	Gastric	stomach
3	chr2:55329600-55342600	Weak transcription	NHEK	skin
4	chr2:55332000-55343400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr2:55334400-55340800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr2:55334800-55339400	Enhancers	Pancreatic Islets	Pancreatic Islet
7	chr2:55335400-55341000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
8	chr2:55336600-55340000	Enhancers	ES-I3 Cell Line	embryonic stem cell
9	chr2:55337000-55339400	Weak transcription	Fetal Brain Female	brain
10	chr2:55337000-55340000	Weak transcription	Fetal Kidney	kidney
11	chr2:55337200-55341000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr2:55337200-55351000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr2:55337400-55342800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr2:55337400-55342800	Weak transcription	HMEC	breast
15	chr2:55338200-55339600	Enhancers	Colon Smooth Muscle	Colon
16	chr2:55338200-55341200	Enhancers	Duodenum Smooth Muscle	Duodenum
17	chr2:55338400-55339400	Enhancers	H9 Cell Line	embryonic stem cell
18	chr2:55338400-55339600	Enhancers	HUES64 Cell Line	embryonic stem cell
19	chr2:55338400-55339600	Enhancers	Hela-S3	cervix
20	chr2:55338400-55339800	Enhancers	HUES6 Cell Line	embryonic stem cell
21	chr2:55338400-55339800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr2:55338400-55340200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr2:55338400-55340200	Flanking Active TSS	Brain Cingulate Gyrus	brain
24	chr2:55338400-55340400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr2:55338400-55340600	Enhancers	HUVEC	blood vessel
26	chr2:55338400-55340800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr2:55338400-55341000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
28	chr2:55338400-55341200	Enhancers	Stomach Mucosa	stomach
29	chr2:55338400-55343400	Enhancers	Primary monocytes fromperipheralblood	blood
30	chr2:55338400-55343400	Enhancers	Primary hematopoietic stem cells	blood
31	chr2:55338600-55339400	Enhancers	H1 Cell Line	embryonic stem cell
32	chr2:55338600-55339400	Enhancers	iPS-15b Cell Line	embryonic stem cell
33	chr2:55338600-55339400	Enhancers	iPS-18 Cell Line	embryonic stem cell
34	chr2:55338600-55339400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr2:55338600-55339600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
36	chr2:55338600-55339600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr2:55338600-55339600	Enhancers	HUES48 Cell Line	embryonic stem cell
38	chr2:55338600-55339600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
39	chr2:55338600-55339600	Enhancers	Aorta	Aorta
40	chr2:55338600-55339600	Flanking Active TSS	Brain Substantia Nigra	brain
41	chr2:55338600-55339600	Enhancers	Left Ventricle	heart
42	chr2:55338600-55339600	Flanking Active TSS	A549	lung
43	chr2:55338600-55339600	Flanking Active TSS	NH-A	brain
44	chr2:55338600-55339600	Flanking Active TSS	NHDF-Ad	bronchial
45	chr2:55338600-55339800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr2:55338600-55339800	Enhancers	iPS-20b Cell Line	embryonic stem cell
47	chr2:55338600-55339800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr2:55338600-55339800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr2:55338600-55339800	Enhancers	Lung	lung
50	chr2:55338600-55339800	Flanking Active TSS	Osteobl	bone

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