Variant report

Variant	rs17021962
Chromosome Location	chr2:99426543-99426544
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:99425256..99428076-chr2:99429019..99431103,2	K562	blood:
2	chr2:99412276..99414413-chr2:99425331..99428982,3	MCF-7	breast:
3	chr2:99422357..99424127-chr2:99425278..99427119,2	MCF-7	breast:
4	chr2:99346314..99348268-chr2:99425170..99426808,2	MCF-7	breast:
5	chr2:99408029..99409823-chr2:99425187..99427144,2	MCF-7	breast:
6	chr2:99346420..99348928-chr2:99424461..99427357,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000071073	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs1599956	0.92[AMR][1000 genomes]
rs17022042	0.90[AMR][1000 genomes]
rs17022046	0.90[AMR][1000 genomes]
rs17022049	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs4571099	0.90[AMR][1000 genomes]
rs4851168	0.90[AMR][1000 genomes]
rs4851169	0.90[AMR][1000 genomes]
rs59878807	0.90[AMR][1000 genomes]
rs72957614	0.90[AMR][1000 genomes]
rs72958693	0.97[AMR][1000 genomes]
rs925883	1.00[CHB][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs925884	0.95[AMR][1000 genomes]
rs925885	0.92[AMR][1000 genomes]
rs956166	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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

No data

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:99414000-99426600	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr2:99418000-99442200	Weak transcription	Stomach Mucosa	stomach
3	chr2:99420800-99426800	Enhancers	Fetal Thymus	thymus
4	chr2:99421200-99427200	Enhancers	Breast Myoepithelial Primary Cells	Breast
5	chr2:99422800-99426600	Weak transcription	Aorta	Aorta
6	chr2:99423000-99432200	Weak transcription	Right Atrium	heart
7	chr2:99423200-99427000	Weak transcription	Fetal Kidney	kidney
8	chr2:99423400-99439200	Weak transcription	Duodenum Mucosa	Duodenum
9	chr2:99423600-99439200	Weak transcription	Brain Angular Gyrus	brain
10	chr2:99423800-99426600	Weak transcription	Spleen	Spleen
11	chr2:99423800-99434200	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr2:99424000-99426600	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr2:99424000-99426800	Enhancers	Primary neutrophils fromperipheralblood	blood
14	chr2:99424000-99432000	Weak transcription	Right Ventricle	heart
15	chr2:99424000-99435600	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr2:99424000-99438400	Weak transcription	Pancreas	Pancrea
17	chr2:99424800-99434800	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr2:99425400-99427200	Enhancers	HepG2	liver
19	chr2:99425600-99426600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr2:99426000-99426800	Enhancers	Brain Anterior Caudate	brain
21	chr2:99426200-99426800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr2:99426200-99426800	Enhancers	Brain Hippocampus Middle	brain
23	chr2:99426200-99426800	Enhancers	HMEC	breast
24	chr2:99426400-99426600	Flanking Active TSS	Lung	lung
25	chr2:99426400-99426800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr2:99426400-99426800	Enhancers	Esophagus	oesophagus
27	chr2:99426400-99426800	Genic enhancers	Fetal Intestine Small	intestine
28	chr2:99426400-99426800	Enhancers	Gastric	stomach
29	chr2:99426400-99427000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr2:99426400-99427400	Enhancers	Sigmoid Colon	Sigmoid Colon
31	chr2:99426400-99427600	Enhancers	Fetal Intestine Large	intestine

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