Variant report

Variant	rs2348477
Chromosome Location	chr2:20400107-20400108
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:20310034..20311974-chr2:20398183..20400238,2	MCF-7	breast:
2	chr2:20393923..20396830-chr2:20398334..20400195,2	K562	blood:
3	chr2:20398170..20400428-chr2:20406801..20409659,2	K562	blood:
4	chr2:20336087..20338079-chr2:20398729..20401526,2	MCF-7	breast:
5	chr2:20398745..20400320-chr2:20644173..20646970,2	MCF-7	breast:
6	chr2:20305860..20308769-chr2:20399902..20401753,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000234378	Chromatin interaction
ENSG00000143878	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs11096646	0.82[ASN][1000 genomes]
rs11895809	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12615923	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13016862	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2348475	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2348478	0.87[ASN][1000 genomes]
rs35363812	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35811865	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35830553	0.81[ASN][1000 genomes]
rs35973557	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs36027823	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4350703	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4432408	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6742663	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6742681	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6749689	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6756290	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[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	nsv1012841	chr2:20328894-20415168	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv1000323	chr2:20336237-20419923	Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:20386200-20401400	Weak transcription	Spleen	Spleen
2	chr2:20386600-20401400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr2:20388600-20400400	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr2:20389200-20413600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr2:20389800-20400400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr2:20390600-20400200	Weak transcription	HMEC	breast
7	chr2:20391000-20403600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr2:20391600-20400400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr2:20391600-20400600	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr2:20391600-20400600	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr2:20391600-20400800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr2:20391600-20402400	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr2:20391600-20404800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr2:20391800-20400600	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr2:20391800-20402200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr2:20391800-20423200	Weak transcription	Right Atrium	heart
17	chr2:20392000-20400600	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr2:20392800-20401600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr2:20394400-20400200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr2:20395600-20400400	Enhancers	Liver	Liver
21	chr2:20395600-20403000	Weak transcription	Rectal Smooth Muscle	rectum
22	chr2:20395800-20400800	Enhancers	Stomach Mucosa	stomach
23	chr2:20396000-20400400	Enhancers	NHEK	skin
24	chr2:20396400-20400200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr2:20396400-20400600	Weak transcription	Fetal Brain Female	brain
26	chr2:20396400-20407000	Weak transcription	Small Intestine	intestine
27	chr2:20396600-20400400	Weak transcription	A549	lung
28	chr2:20397000-20400400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr2:20397200-20400600	Weak transcription	Fetal Muscle Leg	muscle
30	chr2:20398000-20412200	Weak transcription	NH-A	brain
31	chr2:20398400-20401600	Weak transcription	Pancreas	Pancrea
32	chr2:20398600-20406200	Weak transcription	GM12878-XiMat	blood
33	chr2:20399000-20400400	Weak transcription	Lung	lung
34	chr2:20399000-20400600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr2:20399000-20400600	Weak transcription	Brain Germinal Matrix	brain
36	chr2:20399000-20401200	Weak transcription	Sigmoid Colon	Sigmoid Colon
37	chr2:20399000-20401400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr2:20399000-20401600	Weak transcription	NHLF	lung
39	chr2:20399000-20402000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr2:20399200-20400400	Weak transcription	Fetal Intestine Large	intestine
41	chr2:20399200-20400600	Weak transcription	Rectal Mucosa Donor 29	rectum
42	chr2:20399200-20401200	Weak transcription	Rectal Mucosa Donor 31	rectum
43	chr2:20399200-20401400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
44	chr2:20399400-20400400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr2:20399400-20400400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr2:20399400-20400400	Weak transcription	Gastric	stomach
47	chr2:20399400-20401000	Weak transcription	HepG2	liver
48	chr2:20399400-20408400	Weak transcription	NHDF-Ad	bronchial
49	chr2:20399600-20400200	Weak transcription	Placenta	Placenta
50	chr2:20399600-20400200	Weak transcription	Fetal Stomach	stomach

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