Variant report

Variant	rs12469616
Chromosome Location	chr2:99317188-99317189
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:99299792..99302673-chr2:99315201..99317831,2	MCF-7	breast:
2	chr2:99316162..99318899-chr2:99339583..99342162,2	MCF-7	breast:

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10172913	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10496329	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12464653	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12467276	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12468086	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2309434	0.81[ASN][1000 genomes]
rs2871235	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55633363	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs55646762	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs56027617	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs56354279	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs56363239	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56375699	0.81[ASN][1000 genomes]
rs62158010	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs62158015	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs62158019	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62158020	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62158022	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6742760	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs882164	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][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	nsv1013941	chr2:99116255-99317933	Weak transcription Strong transcription Genic enhancers Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv535834	chr2:99116255-99317933	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
3	nsv1011278	chr2:99280928-99638376	Weak transcription Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv535835	chr2:99280928-99638376	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	nsv2841	chr2:99296874-99342362	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:99249800-99318000	Weak transcription	Psoas Muscle	Psoas
2	chr2:99293400-99325200	Weak transcription	Primary hematopoietic stem cells	blood
3	chr2:99294400-99318600	Weak transcription	Spleen	Spleen
4	chr2:99295000-99325200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr2:99302400-99318400	Weak transcription	Ovary	ovary
6	chr2:99303200-99336400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
7	chr2:99304000-99318800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr2:99308000-99317800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr2:99309800-99318600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr2:99310000-99317800	Enhancers	Primary T helper cells PMA-I stimulated	--
11	chr2:99310800-99318000	Weak transcription	Primary B cells from peripheral blood	blood
12	chr2:99310800-99318400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr2:99310800-99318400	Weak transcription	Fetal Thymus	thymus
14	chr2:99310800-99320200	Weak transcription	Thymus	Thymus
15	chr2:99311400-99320800	Weak transcription	Dnd41	blood
16	chr2:99312200-99317600	Weak transcription	Colon Smooth Muscle	Colon
17	chr2:99312200-99317600	Weak transcription	Rectal Smooth Muscle	rectum
18	chr2:99312600-99317600	Enhancers	Rectal Mucosa Donor 31	rectum
19	chr2:99313000-99318400	Weak transcription	Primary neutrophils fromperipheralblood	blood
20	chr2:99313000-99327000	Weak transcription	Monocytes-CD14+_RO01746	blood
21	chr2:99313200-99318200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr2:99313200-99326600	Weak transcription	Primary monocytes fromperipheralblood	blood
23	chr2:99313800-99317600	Weak transcription	Stomach Smooth Muscle	stomach
24	chr2:99314000-99317600	Weak transcription	Brain Angular Gyrus	brain
25	chr2:99314000-99317800	Weak transcription	Brain Hippocampus Middle	brain
26	chr2:99314200-99317600	Weak transcription	Brain Cingulate Gyrus	brain
27	chr2:99314200-99317600	Weak transcription	Fetal Kidney	kidney
28	chr2:99314200-99322000	Enhancers	Fetal Intestine Small	intestine
29	chr2:99314400-99317400	Enhancers	Left Ventricle	heart
30	chr2:99314400-99317800	Weak transcription	Brain Substantia Nigra	brain
31	chr2:99314400-99318600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr2:99314800-99317600	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr2:99315000-99322200	Enhancers	Fetal Intestine Large	intestine
34	chr2:99315200-99318000	Weak transcription	Brain Anterior Caudate	brain
35	chr2:99315400-99317400	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr2:99315400-99319000	Enhancers	HUVEC	blood vessel
37	chr2:99315400-99319400	Enhancers	Sigmoid Colon	Sigmoid Colon
38	chr2:99315800-99317600	Weak transcription	Fetal Heart	heart
39	chr2:99315800-99317600	Weak transcription	HMEC	breast
40	chr2:99315800-99318200	Weak transcription	Right Atrium	heart
41	chr2:99316000-99317400	Enhancers	Primary T cells fromperipheralblood	blood
42	chr2:99316000-99317600	Weak transcription	Stomach Mucosa	stomach
43	chr2:99316000-99317800	Weak transcription	Colonic Mucosa	Colon
44	chr2:99316000-99320800	Enhancers	Primary T helper cells fromperipheralblood	blood
45	chr2:99316400-99325000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
46	chr2:99316600-99317400	Enhancers	Pancreas	Pancrea
47	chr2:99316600-99317400	Weak transcription	Rectal Mucosa Donor 29	rectum
48	chr2:99316600-99317400	Weak transcription	HepG2	liver
49	chr2:99316600-99317600	Weak transcription	Skeletal Muscle Female	skeletal muscle
50	chr2:99316600-99317800	Enhancers	Duodenum Mucosa	Duodenum

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