Variant report

Variant	rs28509770
Chromosome Location	chr3:135793657-135793658
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:135785635..135787568-chr3:135791315..135793865,2	K562	blood:
2	chr3:135793213..135794869-chr3:135799628..135802469,2	MCF-7	breast:
3	chr3:135793633..135795378-chr3:136008278..136010126,2	MCF-7	breast:
4	chr3:135793588..135794769-chr3:136470671..136471683,9	MCF-7	breast:
5	chr3:135793014..135797914-chr3:135913586..135916354,4	MCF-7	breast:
6	chr3:135792541..135795811-chr3:136471093..136473458,3	K562	blood:
7	chr3:135793492..135795446-chr3:136469731..136471715,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000261758	Chromatin interaction
ENSG00000174579	Chromatin interaction
ENSG00000118007	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10048942	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10049233	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10512990	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13079205	0.81[EUR][1000 genomes]
rs13082532	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13082684	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1393787	0.84[AMR][1000 genomes]
rs1403763	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28535121	0.87[AMR][1000 genomes]
rs28576629	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs34864445	0.81[EUR][1000 genomes]
rs67589653	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6769762	0.80[AMR][1000 genomes]
rs6775778	0.80[EUR][1000 genomes]
rs6792630	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6793835	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6799056	0.81[EUR][1000 genomes]
rs6799320	0.81[EUR][1000 genomes]
rs6799517	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7628848	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9653930	0.81[EUR][1000 genomes]
rs9834966	0.81[EUR][1000 genomes]
rs9848926	0.82[EUR][1000 genomes]
rs9870122	0.81[EUR][1000 genomes]
rs9881400	0.84[AMR][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	nsv869409	chr3:135649101-136164174	Strong transcription Genic enhancers Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv4023	chr3:135772198-135816635	ZNF genes & repeats Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 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	chr3:135755200-135801400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr3:135761000-135802400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
3	chr3:135765000-135801800	Weak transcription	Esophagus	oesophagus
4	chr3:135768800-135800800	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr3:135770000-135800800	Weak transcription	Fetal Intestine Large	intestine
6	chr3:135771200-135802000	Weak transcription	Brain Germinal Matrix	brain
7	chr3:135771200-135809600	Weak transcription	Gastric	stomach
8	chr3:135774400-135802000	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr3:135775000-135809600	Weak transcription	Fetal Brain Male	brain
10	chr3:135775000-135809600	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr3:135781400-135801600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr3:135781400-135802000	Weak transcription	Fetal Intestine Small	intestine
13	chr3:135781400-135803000	Weak transcription	Right Ventricle	heart
14	chr3:135784200-135805600	Weak transcription	Stomach Mucosa	stomach
15	chr3:135785000-135798400	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr3:135785600-135799000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr3:135785600-135801800	Weak transcription	Pancreas	Pancrea
18	chr3:135788800-135798600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
19	chr3:135790200-135801800	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr3:135790200-135801800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr3:135790200-135801800	Weak transcription	Ovary	ovary
22	chr3:135790200-135802800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr3:135790200-135830800	Weak transcription	Psoas Muscle	Psoas
24	chr3:135790600-135795800	Weak transcription	Right Atrium	heart
25	chr3:135790600-135798600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr3:135790600-135801400	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr3:135790600-135809600	Weak transcription	Colon Smooth Muscle	Colon
28	chr3:135790800-135794200	Weak transcription	Primary monocytes fromperipheralblood	blood
29	chr3:135790800-135794200	Weak transcription	Muscle Satellite Cultured Cells	--
30	chr3:135790800-135796600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr3:135790800-135798400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr3:135790800-135799000	Weak transcription	Rectal Mucosa Donor 29	rectum
33	chr3:135790800-135800400	Weak transcription	Left Ventricle	heart
34	chr3:135790800-135801600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr3:135790800-135801800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr3:135790800-135801800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr3:135790800-135801800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr3:135790800-135801800	Weak transcription	Fetal Muscle Trunk	muscle
39	chr3:135790800-135802000	Weak transcription	Fetal Kidney	kidney
40	chr3:135790800-135802200	Weak transcription	Placenta Amnion	Placenta Amnion
41	chr3:135790800-135802600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr3:135790800-135803000	Weak transcription	NHEK	skin
43	chr3:135790800-135807000	Weak transcription	Brain Inferior Temporal Lobe	brain
44	chr3:135790800-135809400	Weak transcription	Adipose Nuclei	Adipose
45	chr3:135790800-135809600	Weak transcription	Aorta	Aorta
46	chr3:135790800-135809600	Weak transcription	Brain Angular Gyrus	brain
47	chr3:135790800-135809600	Weak transcription	Brain Anterior Caudate	brain
48	chr3:135790800-135809600	Weak transcription	Brain Cingulate Gyrus	brain
49	chr3:135790800-135809600	Weak transcription	Rectal Smooth Muscle	rectum
50	chr3:135791000-135793800	Weak transcription	NHLF	lung

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