Variant report

Variant	rs6540590
Chromosome Location	chr1:210547505-210547506
allele	A/C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:109)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:109 , 50 per page) page: 1 2 3

No.	Distal block	Cell Line	Cell type
1	chr1:210546877..210547690-chr12:49760648..49761536,2	Hela-S3	cervix:
2	chr1:210545931..210548726-chr1:211432289..211435093,3	K562	blood:
3	chr1:59249248..59249750-chr1:210546978..210547575,2	Hela-S3	cervix:
4	chr1:210546264..210548680-chr1:212458394..212460879,2	K562	blood:
5	chr1:210546992..210547626-chr11:111896111..111896727,2	Hela-S3	cervix:
6	chr1:210546852..210547546-chr13:114780579..114781312,2	Hela-S3	cervix:
7	chr1:210546809..210547778-chr8:145013390..145014250,2	Hela-S3	cervix:
8	chr1:25558947..25559517-chr1:210547147..210547678,2	HCT-116	colon:
9	chr1:210546952..210547520-chr6:13574710..13575516,2	Hela-S3	cervix:
10	chr1:210547155..210547688-chr2:32235666..32236437,2	Hela-S3	cervix:
11	chr1:210547129..210547649-chr10:90750625..90751284,2	Hela-S3	cervix:
12	chr1:210313790..210315610-chr1:210545202..210547564,2	MCF-7	breast:
13	chr1:210546830..210547647-chr6:74230041..74231000,3	Hela-S3	cervix:
14	chr1:210546586..210548937-chr14:75987958..75990203,2	MCF-7	breast:
15	chr1:210546994..210547750-chr20:42838590..42839534,2	Hela-S3	cervix:
16	chr1:210547345..210547922-chr5:137673956..137674487,2	Hela-S3	cervix:
17	chr1:210547064..210548029-chr5:36606437..36607100,2	Hela-S3	cervix:
18	chr1:209999396..210002885-chr1:210546190..210548808,3	K562	blood:
19	chr1:45187384..45187912-chr1:210546992..210547543,2	Hela-S3	cervix:
20	chr1:210545478..210547549-chr1:210653820..210655995,2	MCF-7	breast:
21	chr1:210547105..210548013-chr9:134000440..134001164,2	Hela-S3	cervix:
22	chr1:210547187..210547872-chr15:72522615..72523545,2	Hela-S3	cervix:
23	chr1:210546864..210547592-chr20:61371452..61372006,2	Hela-S3	cervix:
24	chr1:210404317..210408653-chr1:210545033..210548956,7	MCF-7	breast:
25	chr1:210546864..210547753-chr2:242254080..242254825,2	Hela-S3	cervix:
26	chr1:210547114..210547897-chr11:3442902..3443771,2	Hela-S3	cervix:
27	chr1:210547225..210547793-chr14:59950357..59951255,2	Hela-S3	cervix:
28	chr1:210547254..210547868-chr17:48276810..48277746,2	Hela-S3	cervix:
29	chr1:210547137..210547720-chr3:149375009..149375884,2	Hela-S3	cervix:
30	chr1:210547287..210547789-chr11:67782156..67782711,2	Hela-S3	cervix:
31	chr1:45187126..45187862-chr1:210547043..210548063,6	HCT-116	colon:
32	chr1:210545315..210547510-chr4:83350545..83352371,2	MCF-7	breast:
33	chr1:210547375..210547892-chr1:212781759..212782426,2	Hela-S3	cervix:
34	chr1:210546886..210547666-chr12:54674127..54674665,2	Hela-S3	cervix:
35	chr1:210547164..210547723-chr12:51663910..51664553,2	Hela-S3	cervix:
36	chr1:210498648..210506320-chr1:210545155..210548300,7	K562	blood:
37	chr1:210546935..210547738-chr8:42396734..42397693,2	Hela-S3	cervix:
38	chr1:121260558..121261438-chr1:210546944..210547747,3	Hela-S3	cervix:
39	chr1:210546948..210547704-chr20:35089394..35090204,2	Hela-S3	cervix:
40	chr1:210547181..210547830-chr16:89883023..89883687,2	Hela-S3	cervix:
41	chr1:210547074..210547950-chr3:169490734..169491236,2	Hela-S3	cervix:
42	chr1:210547214..210547754-chr12:123717301..123717877,2	Hela-S3	cervix:
43	chr1:210546248..210548847-chr6:26026760..26029454,2	K562	blood:
44	chr1:210547106..210547838-chr11:62622652..62623710,3	Hela-S3	cervix:
45	chr1:210544901..210547632-chr20:52822765..52825018,2	MCF-7	breast:
46	chr1:210546634..210547819-chr17:39844578..39845898,4	Hela-S3	cervix:
47	chr1:210546624..210547534-chr5:158690082..158690945,2	Hela-S3	cervix:
48	chr1:210546241..210548615-chr8:134583124..134585653,3	MCF-7	breast:
49	chr1:210547308..210547811-chr12:107167662..107168440,2	Hela-S3	cervix:
50	chr1:210545562..210548349-chr17:56736330..56737949,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000237188	Chromatin interaction
ENSG00000107796	Chromatin interaction
ENSG00000051825	Chromatin interaction
ENSG00000228393	Chromatin interaction
ENSG00000255717	Chromatin interaction
ENSG00000173812	Chromatin interaction
ENSG00000131791	Chromatin interaction
ENSG00000196230	Chromatin interaction
ENSG00000143537	Chromatin interaction
ENSG00000126790	Chromatin interaction
ENSG00000134905	Chromatin interaction
ENSG00000003756	Chromatin interaction
ENSG00000135486	Chromatin interaction
ENSG00000067225	Chromatin interaction
ENSG00000080845	Chromatin interaction
ENSG00000233455	Chromatin interaction
ENSG00000108821	Chromatin interaction
ENSG00000170545	Chromatin interaction
ENSG00000124523	Chromatin interaction
ENSG00000162959	Chromatin interaction
ENSG00000167470	Chromatin interaction
ENSG00000228110	Chromatin interaction
ENSG00000178209	Chromatin interaction
ENSG00000066027	Chromatin interaction
ENSG00000272583	Chromatin interaction
ENSG00000168003	Chromatin interaction
ENSG00000110921	Chromatin interaction
ENSG00000117597	Chromatin interaction
ENSG00000145293	Chromatin interaction
ENSG00000158402	Chromatin interaction
ENSG00000199377	Chromatin interaction
ENSG00000054392	Chromatin interaction
ENSG00000162772	Chromatin interaction
ENSG00000176055	Chromatin interaction
ENSG00000071655	Chromatin interaction
ENSG00000158710	Chromatin interaction
ENSG00000018408	Chromatin interaction
ENSG00000202077	Chromatin interaction
ENSG00000139428	Chromatin interaction
ENSG00000085274	Chromatin interaction
ENSG00000113013	Chromatin interaction
ENSG00000119969	Chromatin interaction
ENSG00000166492	Chromatin interaction
ENSG00000130119	Chromatin interaction
ENSG00000113356	Chromatin interaction
ENSG00000143878	Chromatin interaction
ENSG00000153487	Chromatin interaction
ENSG00000156508	Chromatin interaction
ENSG00000261220	Chromatin interaction
ENSG00000187741	Chromatin interaction
ENSG00000120709	Chromatin interaction
ENSG00000070950	Chromatin interaction
ENSG00000187837	Chromatin interaction
ENSG00000143473	Chromatin interaction
ENSG00000091651	Chromatin interaction
ENSG00000163719	Chromatin interaction
ENSG00000231752	Chromatin interaction
ENSG00000185670	Chromatin interaction
ENSG00000138376	Chromatin interaction
ENSG00000008513	Chromatin interaction
ENSG00000141232	Chromatin interaction
ENSG00000259006	Chromatin interaction
ENSG00000168575	Chromatin interaction
ENSG00000139190	Chromatin interaction
ENSG00000162757	Chromatin interaction
ENSG00000150768	Chromatin interaction
ENSG00000079215	Chromatin interaction
ENSG00000026103	Chromatin interaction
ENSG00000152795	Chromatin interaction
ENSG00000115677	Chromatin interaction
ENSG00000164332	Chromatin interaction
ENSG00000156127	Chromatin interaction
ENSG00000082497	Chromatin interaction
ENSG00000185305	Chromatin interaction
ENSG00000065911	Chromatin interaction
ENSG00000157557	Chromatin interaction
ENSG00000158636	Chromatin interaction
ENSG00000086061	Chromatin interaction
ENSG00000124529	Chromatin interaction
ENSG00000123352	Chromatin interaction
ENSG00000203706	Chromatin interaction
ENSG00000102119	Chromatin interaction
ENSG00000266559	Chromatin interaction
ENSG00000132823	Chromatin interaction
ENSG00000117595	Chromatin interaction
ENSG00000111785	Chromatin interaction
ENSG00000229980	Chromatin interaction
ENSG00000069329	Chromatin interaction
ENSG00000222894	Chromatin interaction
ENSG00000168385	Chromatin interaction
ENSG00000050130	Chromatin interaction
ENSG00000117625	Chromatin interaction
ENSG00000006534	Chromatin interaction
ENSG00000222724	Chromatin interaction
ENSG00000176209	Chromatin interaction
ENSG00000001631	Chromatin interaction
ENSG00000137074	Chromatin interaction
ENSG00000162639	Chromatin interaction
ENSG00000130921	Chromatin interaction
ENSG00000034510	Chromatin interaction
ENSG00000255135	Chromatin interaction
ENSG00000183258	Chromatin interaction
ENSG00000201524	Chromatin interaction
ENSG00000101132	Chromatin interaction
ENSG00000126883	Chromatin interaction
ENSG00000117614	Chromatin interaction
ENSG00000184260	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10489387	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11119480	0.93[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1883655	0.93[CHB][hapmap];0.93[JPT][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2066721	0.84[CEU][hapmap];0.88[EUR][1000 genomes]
rs2103691	0.81[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2143590	0.80[ASN][1000 genomes]
rs2294844	0.87[CHB][hapmap];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2294847	0.93[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2294848	0.93[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3765864	0.85[ASN][1000 genomes]
rs3765867	0.94[CHB][hapmap];0.85[ASN][1000 genomes]
rs3765868	0.85[ASN][1000 genomes]
rs3765869	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3765873	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3765880	0.81[CEU][hapmap];0.93[CHB][hapmap];0.93[JPT][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3819987	0.93[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4336853	0.81[CEU][hapmap];0.94[CHB][hapmap];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4844522	0.84[CEU][hapmap];0.89[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs4845010	0.81[CHB][hapmap];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs589027	0.87[CHB][hapmap];0.93[JPT][hapmap];0.82[ASN][1000 genomes]
rs590883	0.82[ASN][1000 genomes]
rs6540591	0.85[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs684767	0.87[CHB][hapmap];0.93[JPT][hapmap];0.83[ASN][1000 genomes]
rs761170	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs761172	0.93[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs764585	0.94[CHB][hapmap];0.86[JPT][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs910028	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs910033	0.84[CEU][hapmap];0.87[EUR][1000 genomes]
rs9970232	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv8769	chr1:210403509-210564588	Enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	126 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:210529600-210586000	Weak transcription	Pancreas	Pancrea
2	chr1:210536800-210551000	Weak transcription	Right Ventricle	heart
3	chr1:210536800-210558800	Weak transcription	Fetal Stomach	stomach
4	chr1:210537000-210550600	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr1:210538400-210565600	Weak transcription	Esophagus	oesophagus
6	chr1:210540800-210549600	Weak transcription	HSMMtube	muscle
7	chr1:210541000-210550000	Weak transcription	Brain Anterior Caudate	brain
8	chr1:210543200-210548000	Weak transcription	HSMM	muscle
9	chr1:210543200-210549800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr1:210543200-210555800	Weak transcription	Right Atrium	heart
11	chr1:210543200-210565200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr1:210543400-210551000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr1:210545200-210548200	Enhancers	Hela-S3	cervix
14	chr1:210545400-210547600	Enhancers	H1 Cell Line	embryonic stem cell
15	chr1:210545400-210548600	Enhancers	HUES6 Cell Line	embryonic stem cell
16	chr1:210545800-210548800	Enhancers	NHDF-Ad	bronchial
17	chr1:210546000-210547600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr1:210546000-210548000	Weak transcription	HMEC	breast
19	chr1:210546000-210550200	Enhancers	Muscle Satellite Cultured Cells	--
20	chr1:210546400-210549200	Enhancers	Osteobl	bone
21	chr1:210546600-210548400	Enhancers	NHEK	skin
22	chr1:210546600-210548600	Enhancers	Primary monocytes fromperipheralblood	blood
23	chr1:210546600-210566200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr1:210546800-210547800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr1:210546800-210547800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr1:210546800-210547800	Flanking Active TSS	HepG2	liver
27	chr1:210546800-210548000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
28	chr1:210546800-210548400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
29	chr1:210546800-210548400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr1:210546800-210548400	Enhancers	HUVEC	blood vessel
31	chr1:210546800-210548400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
32	chr1:210546800-210548400	Enhancers	NH-A	brain
33	chr1:210546800-210548600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr1:210547000-210547600	Enhancers	Primary T helper naive cells from peripheral blood	blood
35	chr1:210547000-210547600	Weak transcription	Fetal Intestine Small	intestine
36	chr1:210547000-210547800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr1:210547000-210547800	Enhancers	Fetal Kidney	kidney
38	chr1:210547000-210548200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
39	chr1:210547000-210548400	Enhancers	Cortex derived primary cultured neurospheres	brain
40	chr1:210547000-210548600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
41	chr1:210547200-210547600	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr1:210547200-210548000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
43	chr1:210547200-210548200	Active TSS	A549	lung
44	chr1:210547200-210548400	Enhancers	HUES64 Cell Line	embryonic stem cell
45	chr1:210547200-210548600	Enhancers	HUES48 Cell Line	embryonic stem cell
46	chr1:210547200-210549800	Weak transcription	NHLF	lung
47	chr1:210547200-210550000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr1:210547200-210550000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr1:210547200-210550400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr1:210547200-210550800	Weak transcription	H9 Cell Line	embryonic stem cell

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