Variant report

Variant	rs6816882
Chromosome Location	chr4:6997396-6997397
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:6997053..6999861-chr4:7067007..7069346,2	K562	blood:
2	chr4:6910242..6912678-chr4:6994521..6998393,5	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TADA2B-1	chr4:6997068-6997474	ENSG00000187904.3

Variant related genes	Relation type
ENSG00000109519	Chromatin interaction
ENSG00000132405	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10012590	0.86[ASN][1000 genomes]
rs10025310	0.86[ASN][1000 genomes]
rs10516181	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10937772	0.88[ASN][1000 genomes]
rs10937774	0.83[AMR][1000 genomes]
rs10937776	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11732898	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11938701	0.86[ASN][1000 genomes]
rs11944897	0.86[ASN][1000 genomes]
rs12503027	0.86[ASN][1000 genomes]
rs12642852	0.85[EUR][1000 genomes]
rs13107989	0.86[ASN][1000 genomes]
rs13122119	0.80[ASN][1000 genomes]
rs13135912	0.88[EUR][1000 genomes]
rs13148395	0.86[ASN][1000 genomes]
rs13149411	0.80[ASN][1000 genomes]
rs2301817	0.86[ASN][1000 genomes]
rs2301818	0.80[ASN][1000 genomes]
rs2301819	0.80[ASN][1000 genomes]
rs2359194	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3188939	0.86[ASN][1000 genomes]
rs34219101	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34221933	0.86[ASN][1000 genomes]
rs34335938	0.80[ASN][1000 genomes]
rs34463709	0.80[ASN][1000 genomes]
rs34481892	0.80[ASN][1000 genomes]
rs34959511	0.80[ASN][1000 genomes]
rs35170004	0.80[ASN][1000 genomes]
rs3857171	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3892490	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3894945	0.86[ASN][1000 genomes]
rs4234791	0.80[ASN][1000 genomes]
rs4234793	0.86[ASN][1000 genomes]
rs4296677	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4428285	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4458452	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4544710	0.86[ASN][1000 genomes]
rs4645214	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4689059	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4689060	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4689563	0.80[ASN][1000 genomes]
rs4689564	0.80[ASN][1000 genomes]
rs4689565	0.80[ASN][1000 genomes]
rs4689568	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4689573	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4689575	0.86[ASN][1000 genomes]
rs4689579	0.80[ASN][1000 genomes]
rs55822670	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62289166	0.86[ASN][1000 genomes]
rs66530709	0.80[ASN][1000 genomes]
rs66640699	0.80[ASN][1000 genomes]
rs66931928	0.80[ASN][1000 genomes]
rs66992702	0.80[ASN][1000 genomes]
rs6811496	0.86[ASN][1000 genomes]
rs6818744	0.93[ASN][1000 genomes]
rs6831129	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6834102	0.86[ASN][1000 genomes]
rs6840780	0.86[ASN][1000 genomes]
rs6854776	0.86[ASN][1000 genomes]
rs7655563	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7655773	0.86[ASN][1000 genomes]
rs7658198	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7661462	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7661952	0.86[ASN][1000 genomes]
rs7673901	0.86[ASN][1000 genomes]
rs7685667	0.86[ASN][1000 genomes]
rs7693321	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8180337	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv878530	chr4:6888932-7058473	Strong transcription Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	esv34033	chr4:6973270-7390621	Weak transcription Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	esv2757919	chr4:6988148-7269901	Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
4	esv2759221	chr4:6988148-7269901	Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
5	nsv428436	chr4:6988148-7269901	Bivalent Enhancer Weak transcription Bivalent/Poised TSS Active TSS Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:6989800-6998000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr4:6990000-6997400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr4:6990400-7008800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr4:6991000-7021800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr4:6991400-7000800	Weak transcription	Colonic Mucosa	Colon
6	chr4:6991600-7000000	Weak transcription	Hela-S3	cervix
7	chr4:6993200-6999000	Strong transcription	Dnd41	blood
8	chr4:6993200-7006800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr4:6993800-6998800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr4:6993800-7008400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
11	chr4:6994000-6998000	Weak transcription	Aorta	Aorta
12	chr4:6994000-6998200	Weak transcription	Ovary	ovary
13	chr4:6994000-7000200	Weak transcription	Primary hematopoietic stem cells	blood
14	chr4:6994000-7005200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr4:6994000-7008600	Strong transcription	HUES6 Cell Line	embryonic stem cell
16	chr4:6994000-7035600	Strong transcription	Fetal Stomach	stomach
17	chr4:6994000-7043200	Weak transcription	Right Atrium	heart
18	chr4:6994200-6998400	Weak transcription	Small Intestine	intestine
19	chr4:6994200-7000400	Weak transcription	Fetal Heart	heart
20	chr4:6994200-7000600	Strong transcription	Fetal Muscle Leg	muscle
21	chr4:6994200-7035400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr4:6994400-6998200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
23	chr4:6994400-6999600	Strong transcription	Primary neutrophils fromperipheralblood	blood
24	chr4:6994400-7000800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr4:6994400-7000800	Weak transcription	Pancreas	Pancrea
26	chr4:6994400-7001000	Strong transcription	Fetal Muscle Trunk	muscle
27	chr4:6994400-7013400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
28	chr4:6994600-6998000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr4:6994600-6998000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
30	chr4:6994600-6998200	Weak transcription	Gastric	stomach
31	chr4:6994600-6998200	Weak transcription	Spleen	Spleen
32	chr4:6994600-6999600	Strong transcription	Primary T cells from cord blood	blood
33	chr4:6994600-6999600	Strong transcription	Monocytes-CD14+_RO01746	blood
34	chr4:6994600-7000200	Strong transcription	Primary T cells fromperipheralblood	blood
35	chr4:6994600-7006800	Strong transcription	Stomach Smooth Muscle	stomach
36	chr4:6994600-7021400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr4:6994800-6998000	Weak transcription	Rectal Mucosa Donor 31	rectum
38	chr4:6994800-6998200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
39	chr4:6994800-6999800	Strong transcription	Primary T helper cells PMA-I stimulated	--
40	chr4:6994800-7000600	Strong transcription	Primary T helper cells fromperipheralblood	blood
41	chr4:6994800-7007600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr4:6995000-6998600	Weak transcription	K562	blood
43	chr4:6995000-6999000	Strong transcription	Adipose Nuclei	Adipose
44	chr4:6995000-7009200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr4:6995000-7020800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr4:6995200-6998200	Weak transcription	Esophagus	oesophagus
47	chr4:6995200-6999800	Strong transcription	Placenta	Placenta
48	chr4:6995200-7000200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
49	chr4:6995200-7000600	Weak transcription	Brain Substantia Nigra	brain
50	chr4:6995200-7000600	Weak transcription	Pancreatic Islets	Pancreatic Islet

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