Variant report

Variant	rs2579506
Chromosome Location	chr2:97207321-97207322
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:97204810..97207371-chr2:97218053..97221683,3	MCF-7	breast:
2	chr2:97205879..97208087-chr2:97212324..97213850,2	K562	blood:
3	chr2:97201312..97206028-chr2:97206579..97208935,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000196843	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs11676886	0.87[CEU][hapmap]
rs11891926	0.87[CEU][hapmap]
rs1866444	0.83[CEU][hapmap]
rs2464915	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2579499	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2579500	0.94[ASW][hapmap];0.83[CHB][hapmap];0.96[GIH][hapmap];0.84[LWK][hapmap];0.99[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2579501	0.87[CEU][hapmap]
rs2579503	0.83[CEU][hapmap]
rs4907200	0.87[CEU][hapmap]
rs56092602	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6576978	0.87[CEU][hapmap]
rs6741277	0.87[CEU][hapmap]
rs7584930	0.87[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933671	chr2:96739308-97652262	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
2	nsv1000780	chr2:96740430-97671395	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
3	nsv535826	chr2:96740430-97671395	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
4	nsv874677	chr2:96756547-97717345	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
5	nsv1001204	chr2:96766559-97728507	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
6	nsv535827	chr2:96766559-97728507	Enhancers Active TSS Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh 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	162 gene(s)	inside rSNPs	diseases
7	esv3460902	chr2:97138421-97459342	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
8	esv3460903	chr2:97138421-97459342	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
9	nsv999871	chr2:97157196-97407711	Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
10	nsv535829	chr2:97157196-97407711	Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2579506	TMEM127	cis	parietal	SCAN
rs2579506	TEKT4	cis	cerebellum	SCAN

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:97203800-97220000	Weak transcription	Muscle Satellite Cultured Cells	--
2	chr2:97204200-97207400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr2:97204200-97213200	Weak transcription	HSMMtube	muscle
4	chr2:97204400-97208200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr2:97204400-97213000	Weak transcription	Ovary	ovary
6	chr2:97204400-97220000	Weak transcription	HSMM	muscle
7	chr2:97204600-97215200	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr2:97204800-97215200	Weak transcription	Liver	Liver
9	chr2:97205200-97207400	Weak transcription	Right Ventricle	heart
10	chr2:97205200-97208200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr2:97205200-97208400	Weak transcription	Colonic Mucosa	Colon
12	chr2:97205200-97210200	Genic enhancers	Skeletal Muscle Female	skeletal muscle
13	chr2:97205200-97213000	Weak transcription	Gastric	stomach
14	chr2:97205200-97213200	Weak transcription	Brain Angular Gyrus	brain
15	chr2:97205200-97213200	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr2:97205200-97214200	Weak transcription	Pancreas	Pancrea
17	chr2:97205400-97208000	Weak transcription	Primary monocytes fromperipheralblood	blood
18	chr2:97205400-97208000	Weak transcription	Aorta	Aorta
19	chr2:97205400-97213200	Weak transcription	Fetal Lung	lung
20	chr2:97205400-97215400	Weak transcription	HepG2	liver
21	chr2:97205600-97207600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr2:97205600-97207600	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr2:97205600-97211800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr2:97205600-97212200	Weak transcription	Small Intestine	intestine
25	chr2:97205600-97213000	Enhancers	Primary T helper naive cells from peripheral blood	blood
26	chr2:97205600-97213600	Genic enhancers	Primary T cells fromperipheralblood	blood
27	chr2:97205800-97207600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr2:97205800-97207600	Enhancers	Osteobl	bone
29	chr2:97205800-97213000	Weak transcription	Rectal Mucosa Donor 29	rectum
30	chr2:97205800-97213200	Weak transcription	Fetal Intestine Small	intestine
31	chr2:97205800-97213400	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
32	chr2:97205800-97215000	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
33	chr2:97205800-97220000	Weak transcription	Primary B cells from cord blood	blood
34	chr2:97206000-97207400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr2:97206000-97208200	Weak transcription	Stomach Smooth Muscle	stomach
36	chr2:97206000-97211800	Weak transcription	HUVEC	blood vessel
37	chr2:97206000-97212600	Weak transcription	Right Atrium	heart
38	chr2:97206000-97213000	Weak transcription	Rectal Smooth Muscle	rectum
39	chr2:97206000-97213200	Weak transcription	Rectal Mucosa Donor 31	rectum
40	chr2:97206000-97218800	Strong transcription	Monocytes-CD14+_RO01746	blood
41	chr2:97206000-97220000	Weak transcription	Fetal Heart	heart
42	chr2:97206200-97207400	Weak transcription	Primary hematopoietic stem cells	blood
43	chr2:97206200-97207400	Weak transcription	Brain Hippocampus Middle	brain
44	chr2:97206200-97207400	Weak transcription	Duodenum Smooth Muscle	Duodenum
45	chr2:97206200-97207400	Weak transcription	Fetal Muscle Trunk	muscle
46	chr2:97206200-97207400	Weak transcription	Placenta	Placenta
47	chr2:97206200-97207600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr2:97206200-97207600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr2:97206200-97207600	Weak transcription	Fetal Stomach	stomach
50	chr2:97206200-97207600	Weak transcription	Lung	lung

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