Variant report

Variant	rs6741728
Chromosome Location	chr2:153268746-153268747
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:153265041..153269898-chr2:153270458..153273464,4	K562	blood:

Extended variants
information (count: 19 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10174137	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13007956	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13026858	1.00[CEU][hapmap];1.00[TSI][hapmap]
rs13398440	1.00[CEU][hapmap]
rs13425532	1.00[CEU][hapmap]
rs16831007	1.00[CHB][hapmap];0.85[CHD][hapmap]
rs16831009	1.00[CHB][hapmap];0.85[CHD][hapmap]
rs16831018	1.00[CHB][hapmap];0.85[CHD][hapmap]
rs16831034	1.00[CHB][hapmap]
rs2346199	1.00[CEU][hapmap]
rs34471014	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4664107	1.00[CHB][hapmap];0.85[CHD][hapmap]
rs6434017	1.00[CEU][hapmap]
rs6740909	1.00[CEU][hapmap]
rs73967989	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834419	chr2:153179420-153381476	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
2	nsv1005012	chr2:153206764-153273886	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	esv3693436	chr2:153219836-153479857	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv875291	chr2:153251742-153339823	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6741728	RNF122	trans	brain	seeQTL
rs6741728	CDH23	trans	brain	seeQTL

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:153247400-153277600	Weak transcription	Fetal Intestine Small	intestine
2	chr2:153252000-153269800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr2:153261800-153268800	Enhancers	iPS-18 Cell Line	embryonic stem cell
4	chr2:153263000-153268800	Enhancers	iPS-20b Cell Line	embryonic stem cell
5	chr2:153264000-153268800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr2:153264200-153268800	Enhancers	ES-I3 Cell Line	embryonic stem cell
7	chr2:153264200-153288200	Weak transcription	Stomach Smooth Muscle	stomach
8	chr2:153264400-153269400	Weak transcription	HSMMtube	muscle
9	chr2:153264400-153269600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr2:153264400-153270200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr2:153264400-153271200	Weak transcription	Aorta	Aorta
12	chr2:153264400-153274800	Enhancers	Brain Anterior Caudate	brain
13	chr2:153264400-153278000	Weak transcription	Fetal Kidney	kidney
14	chr2:153264600-153269800	Weak transcription	Colon Smooth Muscle	Colon
15	chr2:153264600-153271800	Weak transcription	Right Atrium	heart
16	chr2:153264600-153277200	Enhancers	A549	lung
17	chr2:153265000-153269600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr2:153265200-153274800	Weak transcription	Fetal Brain Male	brain
19	chr2:153265200-153278000	Weak transcription	Fetal Lung	lung
20	chr2:153265800-153272000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr2:153266000-153268800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr2:153266000-153268800	Enhancers	Pancreas	Pancrea
23	chr2:153266000-153268800	Enhancers	Hela-S3	cervix
24	chr2:153266000-153269000	Enhancers	HMEC	breast
25	chr2:153266000-153270400	Enhancers	HUES48 Cell Line	embryonic stem cell
26	chr2:153266000-153272800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr2:153266000-153278800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
28	chr2:153266200-153268800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr2:153266200-153272600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
30	chr2:153266200-153279000	Enhancers	Brain Angular Gyrus	brain
31	chr2:153266400-153268800	Enhancers	Primary monocytes fromperipheralblood	blood
32	chr2:153266600-153268800	Enhancers	Breast Myoepithelial Primary Cells	Breast
33	chr2:153266600-153268800	Enhancers	Primary hematopoietic stem cells short term culture	blood
34	chr2:153266600-153270200	Enhancers	Placenta	Placenta
35	chr2:153266600-153270800	Enhancers	Cortex derived primary cultured neurospheres	brain
36	chr2:153266800-153270200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr2:153267000-153270200	Enhancers	HUVEC	blood vessel
38	chr2:153267000-153272000	Enhancers	NHEK	skin
39	chr2:153267000-153277000	Weak transcription	NHLF	lung
40	chr2:153267000-153278800	Enhancers	Brain Cingulate Gyrus	brain
41	chr2:153267000-153279200	Enhancers	Brain Substantia Nigra	brain
42	chr2:153267200-153269400	Enhancers	Brain Inferior Temporal Lobe	brain
43	chr2:153267200-153269600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr2:153267200-153271000	Enhancers	HepG2	liver
45	chr2:153267200-153271200	Weak transcription	NH-A	brain
46	chr2:153267200-153271600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr2:153267200-153271800	Weak transcription	Gastric	stomach
48	chr2:153267200-153271800	Weak transcription	Lung	lung
49	chr2:153267400-153269000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr2:153267400-153269000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

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