Variant report

Variant	rs6719469
Chromosome Location	chr2:39555899-39555900
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:39554923..39556541-chr2:39556726..39558880,2	MCF-7	breast:
2	chr2:39554819..39557461-chr2:39561282..39564126,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TMEM178-4	chr2:39555172-39558253	l_1814_chr2:39518006-39558253_76bGuttman_hLF

Extended variants
information (count: 84 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs1012689	0.87[ASN][1000 genomes]
rs10185961	0.82[EUR][1000 genomes]
rs10193807	0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10865148	0.88[EUR][1000 genomes]
rs11124671	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11124674	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11124675	0.84[ASN][1000 genomes]
rs11124680	0.84[ASN][1000 genomes]
rs11677383	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11677611	0.80[ASN][1000 genomes]
rs11688033	0.96[ASN][1000 genomes]
rs11688352	0.85[ASN][1000 genomes]
rs12151392	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12162306	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12618944	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12624242	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12712634	0.90[EUR][1000 genomes]
rs12712640	0.81[ASN][1000 genomes]
rs12712642	0.80[ASN][1000 genomes]
rs12997072	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13405577	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1861733	0.90[EUR][1000 genomes]
rs1861734	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2024514	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2302749	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2373528	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2888593	0.83[EUR][1000 genomes]
rs3755171	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3755172	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3755176	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3770662	0.90[ASN][1000 genomes]
rs3770664	0.88[ASN][1000 genomes]
rs3770671	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3770672	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3770673	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3770674	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3815594	0.84[AMR][1000 genomes]
rs4488638	0.81[EUR][1000 genomes]
rs6544214	0.83[EUR][1000 genomes]
rs6544215	0.84[EUR][1000 genomes]
rs6544216	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6709424	0.88[EUR][1000 genomes]
rs6714566	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6717800	0.86[AMR][1000 genomes]
rs6753014	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6753448	0.82[AMR][1000 genomes]
rs7340455	0.86[ASN][1000 genomes]
rs7561630	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7569037	0.90[EUR][1000 genomes]
rs7569492	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7573923	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7581692	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7582848	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7594145	0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7595469	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7597300	0.84[EUR][1000 genomes]
rs7605427	0.87[ASN][1000 genomes]
rs7608958	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9037	0.82[EUR][1000 genomes]
rs9309036	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9309037	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:23 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv873885	chr2:39200198-39573521	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv1010874	chr2:39255376-39604535	Strong transcription Flanking Active TSS Enhancers Active TSS Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
3	nsv535649	chr2:39255376-39604535	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
4	nsv531346	chr2:39263225-39606367	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
5	nsv533348	chr2:39264345-39596169	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
6	nsv1014520	chr2:39270598-39596299	Enhancers Active TSS Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
7	nsv535650	chr2:39270598-39596299	Enhancers Active TSS Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
8	nsv1009379	chr2:39271472-39604535	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
9	nsv581494	chr2:39277851-39626388	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
10	nsv533456	chr2:39281834-39596298	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
11	esv1832414	chr2:39385155-39588797	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
12	esv1827292	chr2:39385155-39675339	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
13	esv1812828	chr2:39396457-39675339	Flanking Active TSS Strong transcription Active TSS Enhancers Weak transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
14	nsv833847	chr2:39410762-39604640	ZNF genes & repeats Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
15	nsv533445	chr2:39412970-39605266	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
16	esv1830024	chr2:39440552-39588797	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
17	nsv873886	chr2:39468676-39573521	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
18	nsv873887	chr2:39468676-39601889	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
19	nsv997934	chr2:39473548-39751029	Enhancers Strong transcription ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
20	esv1809158	chr2:39474679-39588797	Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
21	esv1828851	chr2:39508121-39588797	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
22	nsv873888	chr2:39508830-39573521	Strong transcription Genic enhancers Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
23	esv2762497	chr2:39540753-39566724	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39481000-39580200	Weak transcription	NHEK	skin
2	chr2:39493600-39565800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr2:39504600-39562000	Weak transcription	Psoas Muscle	Psoas
4	chr2:39504800-39565800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr2:39504800-39567200	Weak transcription	Hela-S3	cervix
6	chr2:39505400-39556800	Weak transcription	Thymus	Thymus
7	chr2:39505400-39557200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr2:39505400-39562400	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr2:39516200-39557600	Weak transcription	Gastric	stomach
10	chr2:39517600-39566400	Weak transcription	Primary T helper cells PMA-I stimulated	--
11	chr2:39519800-39562200	Weak transcription	K562	blood
12	chr2:39519800-39583000	Weak transcription	Brain Angular Gyrus	brain
13	chr2:39520000-39556600	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr2:39520000-39586200	Weak transcription	Fetal Kidney	kidney
15	chr2:39520400-39565800	Weak transcription	Rectal Smooth Muscle	rectum
16	chr2:39524000-39583600	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr2:39528200-39562800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr2:39528400-39562800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr2:39528800-39581800	Weak transcription	Brain Germinal Matrix	brain
20	chr2:39531000-39561600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr2:39534000-39586200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr2:39535400-39562600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr2:39536000-39560800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
24	chr2:39537200-39563800	Weak transcription	Spleen	Spleen
25	chr2:39537400-39558200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr2:39537600-39556800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr2:39538800-39572000	Weak transcription	Small Intestine	intestine
28	chr2:39539000-39563000	Weak transcription	HUES6 Cell Line	embryonic stem cell
29	chr2:39539000-39583800	Weak transcription	Brain Anterior Caudate	brain
30	chr2:39539000-39586400	Weak transcription	Pancreas	Pancrea
31	chr2:39540400-39557200	Weak transcription	Colon Smooth Muscle	Colon
32	chr2:39540400-39560400	Weak transcription	Rectal Mucosa Donor 29	rectum
33	chr2:39540400-39561400	Weak transcription	Fetal Brain Female	brain
34	chr2:39541000-39586400	Weak transcription	Lung	lung
35	chr2:39541400-39557200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr2:39541400-39582200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr2:39542000-39562200	Weak transcription	Fetal Brain Male	brain
38	chr2:39542200-39557200	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr2:39542200-39559800	Weak transcription	Brain Hippocampus Middle	brain
40	chr2:39542200-39561600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr2:39542200-39565600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
42	chr2:39543000-39569400	Weak transcription	HUVEC	blood vessel
43	chr2:39545200-39559200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr2:39545400-39585800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr2:39545800-39560400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr2:39546400-39561600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr2:39547800-39559400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr2:39548200-39562200	Weak transcription	Brain Substantia Nigra	brain
49	chr2:39549800-39561600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr2:39550000-39559600	Strong transcription	Breast Myoepithelial Primary Cells	Breast

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