Variant report

Variant	rs55934348
Chromosome Location	chr2:99246885-99246886
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	chr2:99224674..99227884-chr2:99245399..99250153,4	MCF-7	breast:
2	chr2:99241190..99242773-chr2:99244709..99247701,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000115446	Chromatin interaction
ENSG00000183513	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs11887056	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12618769	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12623494	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13416843	0.91[EUR][1000 genomes]
rs17513621	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17513782	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3769693	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3769694	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3769695	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3769696	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3769697	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6741558	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72825704	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72825708	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72825710	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72825711	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72825718	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72825719	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72825720	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72825725	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72825727	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72825732	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72825733	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7560357	0.83[AMR][1000 genomes];0.94[EUR][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	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

No data

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:99227200-99257400	Strong transcription	Monocytes-CD14+_RO01746	blood
2	chr2:99230200-99250600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr2:99231200-99247600	Weak transcription	Brain Angular Gyrus	brain
4	chr2:99231200-99286200	Weak transcription	Stomach Mucosa	stomach
5	chr2:99232400-99249000	Weak transcription	Psoas Muscle	Psoas
6	chr2:99232400-99250600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr2:99232600-99249400	Weak transcription	Aorta	Aorta
8	chr2:99232800-99250000	Strong transcription	Primary T helper cells fromperipheralblood	blood
9	chr2:99233400-99247200	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr2:99233800-99247600	Weak transcription	Spleen	Spleen
11	chr2:99234000-99252800	Weak transcription	Brain Germinal Matrix	brain
12	chr2:99234200-99247600	Weak transcription	Fetal Stomach	stomach
13	chr2:99234400-99247400	Weak transcription	Right Ventricle	heart
14	chr2:99234400-99251000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr2:99234600-99310600	Weak transcription	Small Intestine	intestine
16	chr2:99234800-99248400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr2:99234800-99250800	Weak transcription	Fetal Muscle Leg	muscle
18	chr2:99234800-99264600	Weak transcription	Ovary	ovary
19	chr2:99234800-99296400	Weak transcription	Esophagus	oesophagus
20	chr2:99235000-99247200	Weak transcription	Primary B cells from peripheral blood	blood
21	chr2:99235400-99248800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr2:99235400-99273600	Weak transcription	Fetal Kidney	kidney
23	chr2:99236000-99248800	Weak transcription	Liver	Liver
24	chr2:99236000-99251200	Weak transcription	Fetal Muscle Trunk	muscle
25	chr2:99238000-99247400	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr2:99238200-99247600	Weak transcription	Left Ventricle	heart
27	chr2:99238200-99247600	Weak transcription	Rectal Smooth Muscle	rectum
28	chr2:99238400-99251200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr2:99238600-99247200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
30	chr2:99238600-99247200	Weak transcription	Brain Hippocampus Middle	brain
31	chr2:99238600-99256000	Weak transcription	Primary B cells from cord blood	blood
32	chr2:99238800-99249000	Weak transcription	Brain Substantia Nigra	brain
33	chr2:99239000-99248000	Weak transcription	Placenta	Placenta
34	chr2:99239000-99249000	Weak transcription	Skeletal Muscle Female	skeletal muscle
35	chr2:99239000-99250400	Weak transcription	Primary hematopoietic stem cells	blood
36	chr2:99239200-99247400	Weak transcription	Skeletal Muscle Male	skeletal muscle
37	chr2:99239200-99247600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr2:99239400-99248800	Weak transcription	Colon Smooth Muscle	Colon
39	chr2:99239400-99249000	Weak transcription	HUVEC	blood vessel
40	chr2:99239600-99247400	Weak transcription	Thymus	Thymus
41	chr2:99240000-99247200	Weak transcription	Lung	lung
42	chr2:99240400-99247400	Weak transcription	Colonic Mucosa	Colon
43	chr2:99240400-99247400	Weak transcription	Fetal Intestine Large	intestine
44	chr2:99240400-99248600	Strong transcription	Primary T cells fromperipheralblood	blood
45	chr2:99240400-99248600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
46	chr2:99240600-99247200	Weak transcription	Sigmoid Colon	Sigmoid Colon
47	chr2:99240600-99247400	Weak transcription	Gastric	stomach
48	chr2:99242400-99247200	Weak transcription	HepG2	liver
49	chr2:99243600-99265800	Strong transcription	Duodenum Mucosa	Duodenum
50	chr2:99244200-99249800	Strong transcription	Fetal Thymus	thymus

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