Variant report

Variant	rs55989335
Chromosome Location	chr3:43069294-43069295
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:43068747..43070408-chr3:43073620..43075322,2	MCF-7	breast:

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs11710681	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11711497	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11711635	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11711770	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11718847	0.92[EUR][1000 genomes]
rs12492075	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1523123	0.88[EUR][1000 genomes]
rs1533697	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17075084	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17469356	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3732858	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs537396	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs540864	0.84[EUR][1000 genomes]
rs57079337	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57641345	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs57758537	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs601055	0.84[EUR][1000 genomes]
rs62247069	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62247120	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62247121	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62247124	0.86[EUR][1000 genomes]
rs62247127	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62249581	0.90[EUR][1000 genomes]
rs686464	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72869056	0.90[EUR][1000 genomes]
rs834189	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv460522	chr3:42967597-43175207	Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv590149	chr3:42967597-43175207	Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv432417	chr3:43045796-43098296	ZNF genes & repeats Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:43053600-43073200	Weak transcription	Right Atrium	heart
2	chr3:43059600-43074400	Weak transcription	Lung	lung
3	chr3:43059600-43084600	Weak transcription	Pancreas	Pancrea
4	chr3:43060800-43069600	Weak transcription	Stomach Mucosa	stomach
5	chr3:43061000-43072200	Weak transcription	Liver	Liver
6	chr3:43061000-43080200	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr3:43061800-43073000	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr3:43063000-43077400	Weak transcription	Brain Hippocampus Middle	brain
9	chr3:43063400-43072000	Weak transcription	Stomach Smooth Muscle	stomach
10	chr3:43063600-43072600	Weak transcription	Fetal Muscle Leg	muscle
11	chr3:43063600-43084800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr3:43064000-43077800	Weak transcription	Brain Substantia Nigra	brain
13	chr3:43065200-43072400	Weak transcription	Placenta	Placenta
14	chr3:43065400-43084400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr3:43067400-43076200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr3:43067600-43069800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
17	chr3:43067600-43070800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr3:43067600-43084000	Weak transcription	Aorta	Aorta
19	chr3:43067800-43070000	Weak transcription	Gastric	stomach
20	chr3:43067800-43071000	Weak transcription	Primary T cells fromperipheralblood	blood
21	chr3:43067800-43071000	Weak transcription	Primary T helper cells fromperipheralblood	blood
22	chr3:43067800-43074400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr3:43068000-43070800	Weak transcription	Fetal Thymus	thymus
24	chr3:43068200-43071200	Weak transcription	Primary T helper cells PMA-I stimulated	--
25	chr3:43068200-43076800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
26	chr3:43068800-43069800	Weak transcription	Fetal Intestine Large	intestine
27	chr3:43068800-43070200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr3:43068800-43070800	Weak transcription	Primary T cells from cord blood	blood
29	chr3:43069000-43069600	Weak transcription	Fetal Intestine Small	intestine

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