Variant report

Variant	rs952402
Chromosome Location	chr4:148413080-148413081
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TMEM184C-2	chr4:148407981-148413807	NONHSAT098682

Extended variants
information (count: 79 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs10011966	0.88[CEU][hapmap];0.90[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10024834	0.96[CEU][hapmap];0.90[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10305860	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10305862	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11100963	0.90[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs11722942	0.87[ASN][1000 genomes]
rs11727337	0.87[ASN][1000 genomes]
rs11727397	0.87[ASN][1000 genomes]
rs11730985	0.87[ASN][1000 genomes]
rs11731096	0.83[ASN][1000 genomes]
rs11731097	0.83[ASN][1000 genomes]
rs11731134	0.87[ASN][1000 genomes]
rs12509416	0.95[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs12642328	0.88[ASN][1000 genomes]
rs13109203	0.81[AFR][1000 genomes]
rs13109209	0.85[AFR][1000 genomes]
rs13112065	0.87[ASN][1000 genomes]
rs13127894	0.90[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs13138887	0.82[ASN][1000 genomes]
rs13143677	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13144507	0.89[ASN][1000 genomes]
rs1366688	0.90[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs1400554	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1400558	0.86[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs1400559	0.87[ASN][1000 genomes]
rs1400560	0.87[ASN][1000 genomes]
rs1517134	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1517138	0.87[ASN][1000 genomes]
rs1517139	0.87[ASN][1000 genomes]
rs17474816	0.96[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17474823	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1801708	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1808039	0.88[AFR][1000 genomes]
rs1949375	0.87[ASN][1000 genomes]
rs1996373	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1996374	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2063936	0.87[ASN][1000 genomes]
rs34256803	0.95[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs35686091	0.95[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs4631019	0.85[ASN][1000 genomes]
rs4835081	0.87[ASN][1000 genomes]
rs4835083	0.95[CEU][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4835084	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4835086	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4835401	0.87[ASN][1000 genomes]
rs4835405	0.87[ASN][1000 genomes]
rs4835407	0.87[ASN][1000 genomes]
rs4835410	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56015601	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57886575	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6537479	0.86[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs6537480	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6537482	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6537483	0.96[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6537484	0.86[CHB][hapmap];0.83[JPT][hapmap];0.80[ASN][1000 genomes]
rs6810637	0.80[ASN][1000 genomes]
rs6817469	0.85[ASN][1000 genomes]
rs6819740	0.88[CEU][hapmap];0.91[CHB][hapmap];0.83[JPT][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6820938	0.98[ASN][1000 genomes]
rs6823537	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6835512	0.81[ASN][1000 genomes]
rs6840108	0.90[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs6840756	0.96[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6840784	0.90[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs6848108	0.96[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6853791	0.80[ASN][1000 genomes]
rs6855875	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs702757	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7655670	0.88[CEU][hapmap];0.91[CHB][hapmap];0.83[JPT][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7659823	0.98[ASN][1000 genomes]
rs7663891	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9308218	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs959600	0.87[ASN][1000 genomes]
rs984457	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs984458	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9991584	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[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	nsv830109	chr4:148295061-148468605	Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
2	nsv1028958	chr4:148377752-148793485	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
3	nsv880241	chr4:148411178-148461073	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:148403800-148417600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr4:148404200-148413200	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr4:148404200-148418800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr4:148404200-148419000	Weak transcription	HMEC	breast
5	chr4:148404600-148413200	Weak transcription	Fetal Muscle Leg	muscle
6	chr4:148404600-148419000	Weak transcription	NHLF	lung
7	chr4:148405800-148416000	Weak transcription	Spleen	Spleen
8	chr4:148407000-148413200	Weak transcription	Right Atrium	heart
9	chr4:148408200-148413200	Weak transcription	Fetal Stomach	stomach
10	chr4:148408400-148413200	Weak transcription	Aorta	Aorta
11	chr4:148408400-148416800	Weak transcription	Right Ventricle	heart
12	chr4:148410000-148413200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr4:148410000-148414000	Weak transcription	NHEK	skin
14	chr4:148410200-148413400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr4:148410200-148413400	Weak transcription	Fetal Intestine Small	intestine
16	chr4:148410200-148413600	Weak transcription	NHDF-Ad	bronchial
17	chr4:148410600-148413200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr4:148411200-148415400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr4:148411200-148415600	Weak transcription	Left Ventricle	heart
20	chr4:148411400-148413400	Enhancers	Fetal Heart	heart
21	chr4:148411400-148414000	Weak transcription	Adipose Nuclei	Adipose
22	chr4:148412000-148414000	Enhancers	Ovary	ovary
23	chr4:148412400-148414000	Enhancers	Fetal Lung	lung
24	chr4:148412600-148414600	Enhancers	Fetal Kidney	kidney
25	chr4:148413000-148413400	Enhancers	Stomach Smooth Muscle	stomach
26	chr4:148413000-148413600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr4:148413000-148414200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
28	chr4:148413000-148414400	Enhancers	Osteobl	bone
29	chr4:148413000-148414600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr4:148413000-148414600	Enhancers	NH-A	brain

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