Variant report

Variant	rs4077205
Chromosome Location	chr5:177384649-177384650
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-FAM153C-4	chr5:177384610-177384680	ENSG00000249684.1
2	lnc-FAM153C-4	chr5:177384610-177384680	ENSG00000249684.1
3	lnc-FAM153C-4	chr5:177384610-177384760	ENSG00000249684.1
4	lnc-FAM153C-4	chr5:177384610-177384751	ENSG00000249684.1
5	lnc-FAM153C-5	chr5:177384610-177384979	NONHSAT105484

Extended variants
information (count: 64 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10055278	0.82[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs10060376	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10464116	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10794706	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11249783	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11738026	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11739986	0.95[ASN][1000 genomes]
rs11740554	0.90[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs11741476	0.89[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs11742117	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12186510	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12187456	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13157329	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13157464	0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13157845	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13166313	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs13167457	0.81[AMR][1000 genomes]
rs13178333	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs13190413	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs28401381	0.84[ASN][1000 genomes]
rs4077204	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4077206	0.96[ASN][1000 genomes]
rs4246052	0.86[EUR][1000 genomes]
rs4318803	0.86[EUR][1000 genomes]
rs4540200	0.86[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs4958945	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4958946	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4958947	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4958948	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4958980	0.84[EUR][1000 genomes]
rs4958983	0.86[EUR][1000 genomes]
rs4958995	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4958999	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4959001	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4959002	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4959003	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56268665	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60355061	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62397831	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62397832	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6861547	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6885392	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7341034	0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7705931	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7706237	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7706255	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7718261	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7730346	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7733233	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9764398	0.87[EUR][1000 genomes]
rs9765519	0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1024444	chr5:176751921-177427715	Weak transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	142 gene(s)	inside rSNPs	diseases
2	esv2752795	chr5:176898619-177488281	Active TSS Strong transcription Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	78 gene(s)	inside rSNPs	diseases
3	nsv1030383	chr5:177310325-177571254	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
4	nsv883184	chr5:177311043-177488281	Bivalent/Poised TSS Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv883185	chr5:177357964-177401509	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv521629	chr5:177364884-177396200	Flanking Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv883186	chr5:177376317-177549491	Weak transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
8	nsv883187	chr5:177377400-177419967	ZNF genes & repeats Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	esv2760946	chr5:177379490-177401509	Weak transcription ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	nsv432821	chr5:177380624-177400868	Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
11	nsv517302	chr5:177383782-177400248	Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
12	esv2754618	chr5:177384542-177413659	Enhancers Bivalent Enhancer ZNF genes & repeats Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
13	nsv948342	chr5:177384542-178168737	Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	141 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:177368200-177396400	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr5:177371000-177393000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
3	chr5:177371600-177385200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr5:177371600-177389600	Weak transcription	Brain Germinal Matrix	brain
5	chr5:177371800-177387400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr5:177371800-177387600	Weak transcription	Pancreas	Pancrea
7	chr5:177371800-177387800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr5:177371800-177388200	Weak transcription	Gastric	stomach
9	chr5:177371800-177390200	Weak transcription	Primary T cells from cord blood	blood
10	chr5:177371800-177390800	Weak transcription	Ovary	ovary
11	chr5:177371800-177392800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr5:177371800-177394200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr5:177371800-177394200	Weak transcription	Right Ventricle	heart
14	chr5:177372000-177385200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr5:177372000-177385400	Weak transcription	NHDF-Ad	bronchial
16	chr5:177372200-177390000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr5:177372400-177385600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr5:177372600-177385600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr5:177372600-177388200	Weak transcription	Esophagus	oesophagus
20	chr5:177374400-177385200	Weak transcription	HUES64 Cell Line	embryonic stem cell
21	chr5:177375200-177387600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr5:177375400-177385200	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr5:177375400-177385200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr5:177378000-177388400	Weak transcription	Primary B cells from peripheral blood	blood
25	chr5:177378600-177385200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr5:177378600-177387600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr5:177379200-177385800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr5:177379200-177386000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
29	chr5:177379200-177387600	Weak transcription	NHLF	lung
30	chr5:177379200-177392400	Weak transcription	Primary T cells fromperipheralblood	blood
31	chr5:177383200-177384800	Weak transcription	Primary T helper cells PMA-I stimulated	--
32	chr5:177383800-177393600	Weak transcription	Primary T helper cells fromperipheralblood	blood
33	chr5:177384200-177384800	Strong transcription	HUES48 Cell Line	embryonic stem cell
34	chr5:177384400-177385600	Weak transcription	H9 Cell Line	embryonic stem cell
35	chr5:177384400-177386800	Enhancers	H1 Cell Line	embryonic stem cell
36	chr5:177384600-177384800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
37	chr5:177384600-177385000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

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