Variant report

Variant	rs35199330
Chromosome Location	chr12:29324832-29324833
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RP11-677C1.2.1-3	chr12:29324311-29324983	NONHSAT027482

Extended variants
information (count: 61 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs12811417	1.00[EUR][1000 genomes]
rs12813343	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs12815733	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12816534	1.00[EUR][1000 genomes]
rs12817351	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12819686	1.00[EUR][1000 genomes]
rs12820515	1.00[EUR][1000 genomes]
rs12826306	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12831837	1.00[EUR][1000 genomes]
rs12832977	1.00[EUR][1000 genomes]
rs1496214	0.85[AMR][1000 genomes]
rs34064202	1.00[EUR][1000 genomes]
rs34158620	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34170651	1.00[EUR][1000 genomes]
rs34237455	1.00[EUR][1000 genomes]
rs34270636	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34339523	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34391841	1.00[EUR][1000 genomes]
rs34418975	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs34492685	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34526565	1.00[EUR][1000 genomes]
rs34572599	1.00[EUR][1000 genomes]
rs34601700	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34624113	1.00[EUR][1000 genomes]
rs34685180	1.00[EUR][1000 genomes]
rs34690032	1.00[EUR][1000 genomes]
rs34825983	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34879577	1.00[EUR][1000 genomes]
rs34941964	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34990495	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35002558	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35018848	0.85[AFR][1000 genomes]
rs35039649	1.00[EUR][1000 genomes]
rs35042869	1.00[EUR][1000 genomes]
rs35054952	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35071007	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35100017	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35121122	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35195316	1.00[EUR][1000 genomes]
rs35244320	0.84[AFR][1000 genomes]
rs35426167	1.00[EUR][1000 genomes]
rs35447364	1.00[EUR][1000 genomes]
rs35708989	1.00[EUR][1000 genomes]
rs35736217	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35763553	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35773649	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35776525	1.00[EUR][1000 genomes]
rs35779561	1.00[EUR][1000 genomes]
rs35861754	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71453726	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71453728	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71453729	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7307362	0.86[AFR][1000 genomes]
rs7315584	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7953699	0.85[AMR][1000 genomes]
rs7955386	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7971655	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7972299	1.00[EUR][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	nsv532233	chr12:29009388-29496179	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv995123	chr12:29095272-29571558	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv1053641	chr12:29268813-29854413	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:29317600-29340800	Weak transcription	Left Ventricle	heart
2	chr12:29317800-29326800	Weak transcription	Primary T cells from cord blood	blood
3	chr12:29318200-29326200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr12:29318400-29329600	Weak transcription	NHLF	lung
5	chr12:29321200-29325200	Weak transcription	Rectal Smooth Muscle	rectum
6	chr12:29321800-29327000	Weak transcription	Small Intestine	intestine
7	chr12:29322400-29335600	Weak transcription	Gastric	stomach
8	chr12:29323000-29329600	Weak transcription	Adipose Nuclei	Adipose
9	chr12:29323000-29332400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr12:29323400-29327000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr12:29324000-29325400	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
12	chr12:29324000-29325400	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr12:29324000-29325600	ZNF genes & repeats	Fetal Intestine Small	intestine
14	chr12:29324000-29325800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr12:29324000-29326000	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
16	chr12:29324000-29329600	Weak transcription	Primary hematopoietic stem cells	blood
17	chr12:29324200-29325200	ZNF genes & repeats	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr12:29324200-29325200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr12:29324200-29325200	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland
20	chr12:29324400-29325000	ZNF genes & repeats	H9 Cell Line	embryonic stem cell
21	chr12:29324400-29325000	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
22	chr12:29324400-29325000	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr12:29324400-29325000	ZNF genes & repeats	Brain Germinal Matrix	brain
24	chr12:29324400-29325000	ZNF genes & repeats	Fetal Muscle Leg	muscle
25	chr12:29324400-29325000	ZNF genes & repeats	Fetal Stomach	stomach
26	chr12:29324400-29325000	Strong transcription	Rectal Mucosa Donor 29	rectum
27	chr12:29324400-29325000	ZNF genes & repeats	Dnd41	blood
28	chr12:29324400-29325000	Strong transcription	HUVEC	blood vessel
29	chr12:29324400-29325200	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
30	chr12:29324400-29325200	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr12:29324400-29325200	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr12:29324400-29325200	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr12:29324400-29325200	ZNF genes & repeats	iPS-15b Cell Line	embryonic stem cell
34	chr12:29324400-29325200	Strong transcription	Primary monocytes fromperipheralblood	blood
35	chr12:29324400-29325200	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr12:29324400-29325200	ZNF genes & repeats	Fetal Intestine Large	intestine
37	chr12:29324400-29325200	ZNF genes & repeats	Fetal Muscle Trunk	muscle
38	chr12:29324400-29325200	ZNF genes & repeats	Lung	lung
39	chr12:29324400-29325200	Strong transcription	Rectal Mucosa Donor 31	rectum
40	chr12:29324400-29325200	Genic enhancers	Spleen	Spleen
41	chr12:29324400-29325400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr12:29324400-29325600	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
43	chr12:29324400-29325600	Strong transcription	Sigmoid Colon	Sigmoid Colon
44	chr12:29324600-29325000	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
45	chr12:29324600-29325200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr12:29324600-29325200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr12:29324600-29325200	Strong transcription	Duodenum Mucosa	Duodenum
48	chr12:29324600-29325200	Strong transcription	Monocytes-CD14+_RO01746	blood
49	chr12:29324600-29325400	Strong transcription	Primary neutrophils fromperipheralblood	blood
50	chr12:29324600-29325600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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