Variant report

Variant	rs72854536
Chromosome Location	chr6:28323128-28323129
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:7)
CpG islands
(count:61)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:7 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:28321625-28325043	SK-N-MC	brain:	n/a	n/a
2	CTCF	chr6:28323069-28324565	SK-N-SH	brain:	n/a	n/a
3	POLR2A	chr6:28323116-28323131	HUVEC	blood vessel:	n/a	n/a
4	TEAD4	chr6:28323021-28324330	K562	blood:	n/a	n/a
5	POLR2A	chr6:28321678-28325465	K562	blood:	n/a	n/a
6	POLR2A	chr6:28323016-28323231	Hela-S3	cervix:	n/a	n/a
7	NR2F2	chr6:28321148-28323272	K562	blood:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr6:28323128-28323178	Caco-2	colon:	n/a
2	chr6:28323128-28323178	A549	lung:	n/a
3	chr6:28323128-28323178	T-47D	breast:	n/a
4	chr6:28323128-28323178	PFSK-1	brain:	n/a
5	chr6:28323128-28323178	AG04450	lung:	fetal
6	chr6:28323128-28323178	ovcar-3	ovarian:	n/a
7	chr6:28323128-28323178	SAEC	small airway:	n/a
8	chr6:28323128-28323178	HPAEpiC	pulmonary alveolar:	n/a
9	chr6:28323128-28323178	ECC-1	luminal epithelium:	n/a
10	chr6:28323128-28323178	CMK	blood:	n/a
11	chr6:28323128-28323178	HCT-116	colon:	n/a
12	chr6:28323128-28323178	HAEpiC	amniotic membrane:	n/a
13	chr6:28323128-28323178	AG09319	gingival:	n/a
14	chr6:28323128-28323178	NB4	blood:	n/a
15	chr6:28323128-28323178	SKMC	muscle:	n/a
16	chr6:28323128-28323178	HIPEpiC	eye:	n/a
17	chr6:28323128-28323178	PANC-1	pancreas:	n/a
18	chr6:28323128-28323178	NH-A	brain:	n/a
19	chr6:28323128-28323178	AG09309	skin:	n/a
20	chr6:28323128-28323178	HRPEpiC	eye:	n/a
21	chr6:28323128-28323178	HEEpiC	esophagus:	n/a
22	chr6:28323128-28323178	SK-N-SH	brain:	n/a
23	chr6:28323128-28323178	MCF10A-Er-Src	breast:	n/a
24	chr6:28323128-28323178	RPTEC	kidney:	n/a
25	chr6:28323128-28323178	HNPCEpiC	eye:	n/a
26	chr6:28323128-28323178	LNCaP	prostate:	n/a
27	chr6:28323128-28323178	HRCEpiC	kidney:	n/a
28	chr6:28323128-28323178	Jurkat	blood:	n/a
29	chr6:28323128-28323178	HRE	kidney:	n/a
30	chr6:28323128-28323178	MCF-7	breast:	n/a
31	chr6:28323128-28323178	HCM	heart:	n/a
32	chr6:28323128-28323178	GM12891	blood:	n/a
33	chr6:28323128-28323178	Hepatocyte	liver:	n/a
34	chr6:28323128-28323178	K562	blood:	n/a
35	chr6:28323128-28323178	GM12878	blood:	n/a
36	chr6:28323128-28323178	BE2_C	brain:	n/a
37	chr6:28323128-28323178	HepG2	liver:	n/a
38	chr6:28323128-28323178	GM12892	blood:	n/a
39	chr6:28323128-28323178	HEK293	kidney:	embryo
40	chr6:28323128-28323178	PrEC	prostate:	n/a
41	chr6:28323128-28323178	GM19239	blood:	n/a
42	chr6:28323128-28323178	HCPEpiC	choroid plexus:	n/a
43	chr6:28323128-28323178	H1-hESC	embryonic stem cell:	embryo
44	chr6:28323128-28323178	NHBE	bronchial:	n/a
45	chr6:28323128-28323178	AG10803	skin:	n/a
46	chr6:28323128-28323178	SK-N-MC	brain:	n/a
47	chr6:28323128-28323178	HUVEC	blood vessel:	n/a
48	chr6:28323128-28323178	Hela-S3	cervix:	n/a
49	chr6:28323128-28323178	ProgFib	skin:	n/a
50	chr6:28323128-28323178	HMEC	breast:	n/a

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:28247781..28251138-chr6:28322226..28325499,4	K562	blood:
2	chr6:28183629..28195178-chr6:28316250..28325659,29	K562	blood:
3	chr6:27780093..27783062-chr6:28322537..28324933,2	K562	blood:
4	chr6:27860028..27861689-chr6:28321850..28323929,2	K562	blood:
5	chr6:28182735..28195387-chr6:28315960..28325841,32	K562	blood:
6	chr6:27857264..27863272-chr6:28318615..28325449,9	K562	blood:
7	chr6:28102102..28105139-chr6:28322040..28324310,3	K562	blood:
8	chr6:28314766..28319001-chr6:28320941..28324187,4	MCF-7	breast:
9	chr6:28233021..28237962-chr6:28316234..28324041,9	K562	blood:

No data

Variant related genes	Relation type
ZSCAN31	TF binding region
ZSCAN31	CpG island
ENSG00000233224	Chromatin interaction
ENSG00000197153	Chromatin interaction
ENSG00000197062	Chromatin interaction
ENSG00000196374	Chromatin interaction
ENSG00000137185	Chromatin interaction
ENSG00000196331	Chromatin interaction
ENSG00000137338	Chromatin interaction
ENSG00000182611	Chromatin interaction
ENSG00000189298	Chromatin interaction
ENSG00000269293	Chromatin interaction
ENSG00000176933	Chromatin interaction
ENSG00000261839	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs11546572	1.00[AFR][1000 genomes]
rs2079705	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs28745594	1.00[ASN][1000 genomes]
rs34757087	1.00[ASN][1000 genomes]
rs34951544	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs35062161	1.00[ASN][1000 genomes]
rs35758328	1.00[ASN][1000 genomes]
rs41269285	1.00[AFR][1000 genomes]
rs41269289	1.00[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs41269291	1.00[AFR][1000 genomes]
rs41270579	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs41270589	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs41270596	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4540253	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs62620226	1.00[AFR][1000 genomes]
rs72844204	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs72844212	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs72844218	1.00[AFR][1000 genomes]
rs72844220	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs72844224	1.00[ASN][1000 genomes]
rs72844225	1.00[ASN][1000 genomes]
rs72844226	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs72846777	1.00[AFR][1000 genomes]
rs72846788	1.00[AFR][1000 genomes]
rs72846792	1.00[AFR][1000 genomes]
rs72846802	1.00[AFR][1000 genomes]
rs72849204	1.00[AFR][1000 genomes]
rs72849206	1.00[AFR][1000 genomes]
rs72849210	1.00[AFR][1000 genomes]
rs72849214	1.00[AFR][1000 genomes]
rs72849222	1.00[AFR][1000 genomes]
rs72850297	1.00[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs72850298	1.00[AFR][1000 genomes]
rs72850299	1.00[AFR][1000 genomes]
rs72850300	1.00[AFR][1000 genomes]
rs72850302	1.00[AFR][1000 genomes]
rs72851173	1.00[AFR][1000 genomes]
rs72851179	1.00[AFR][1000 genomes]
rs72851182	1.00[AFR][1000 genomes]
rs72854503	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs72854515	1.00[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs72854521	1.00[AFR][1000 genomes]
rs72854522	1.00[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs72854524	0.87[EUR][1000 genomes]
rs72854525	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs72854527	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs72854531	1.00[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs72854533	1.00[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs72854535	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72854542	1.00[ASN][1000 genomes]
rs72854546	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs72854553	1.00[ASN][1000 genomes]
rs72854556	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7752415	1.00[AFR][1000 genomes];0.87[EUR][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	nsv830620	chr6:28173997-28348033	Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Enhancers Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	51 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28318400-28323600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr6:28318400-28332000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr6:28318400-28350800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr6:28319000-28323200	Weak transcription	Primary B cells from peripheral blood	blood
5	chr6:28319000-28323200	Weak transcription	Small Intestine	intestine
6	chr6:28319200-28323200	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr6:28319200-28323200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr6:28319200-28323200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr6:28319200-28323200	Weak transcription	Fetal Intestine Small	intestine
10	chr6:28319200-28323400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr6:28319200-28323400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr6:28319200-28323600	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr6:28319200-28323600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr6:28319200-28323600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr6:28319400-28323200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
16	chr6:28319400-28323400	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr6:28319400-28323400	Weak transcription	Primary B cells from cord blood	blood
18	chr6:28319400-28323600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
19	chr6:28319600-28323200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr6:28319600-28323200	Weak transcription	Primary T helper cells fromperipheralblood	blood
21	chr6:28319600-28323400	Weak transcription	Fetal Brain Female	brain
22	chr6:28319600-28323400	Weak transcription	Thymus	Thymus
23	chr6:28320800-28323200	Weak transcription	GM12878-XiMat	blood
24	chr6:28321200-28323200	Enhancers	Brain Hippocampus Middle	brain
25	chr6:28321400-28323200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr6:28321600-28323200	Enhancers	Osteobl	bone
27	chr6:28321800-28323200	Enhancers	Adipose Nuclei	Adipose
28	chr6:28321800-28323200	Enhancers	HSMM	muscle
29	chr6:28321800-28323400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
30	chr6:28321800-28323600	Enhancers	Gastric	stomach
31	chr6:28321800-28323600	Enhancers	Spleen	Spleen
32	chr6:28322000-28323200	Enhancers	Breast Myoepithelial Primary Cells	Breast
33	chr6:28322000-28323200	Enhancers	Muscle Satellite Cultured Cells	--
34	chr6:28322000-28323200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr6:28322000-28323200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr6:28322000-28323200	Enhancers	Brain Anterior Caudate	brain
37	chr6:28322000-28323200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
38	chr6:28322000-28323200	Enhancers	Rectal Smooth Muscle	rectum
39	chr6:28322000-28323400	Enhancers	Left Ventricle	heart
40	chr6:28322000-28323400	Enhancers	Pancreas	Pancrea
41	chr6:28322000-28323400	Enhancers	HUVEC	blood vessel
42	chr6:28322000-28323600	Enhancers	Esophagus	oesophagus
43	chr6:28322000-28323600	Enhancers	Psoas Muscle	Psoas
44	chr6:28322000-28323600	Enhancers	Stomach Mucosa	stomach
45	chr6:28322200-28323200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr6:28322200-28323200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr6:28322200-28323200	Enhancers	Fetal Heart	heart
48	chr6:28322200-28323200	Enhancers	HSMMtube	muscle
49	chr6:28322200-28323400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr6:28322200-28323400	Weak transcription	HUES6 Cell Line	embryonic stem cell

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