Variant report

Variant	rs620401
Chromosome Location	chr10:27541113-27541114
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:13)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:13 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TEAD4	chr10:27541015-27541805	H1-hESC	embryonic stem cell:	n/a	n/a
2	CTCF	chr10:27541100-27541250	HFF	foreskin:	n/a	n/a
3	CTCF	chr10:27541080-27541310	HCM	heart:	n/a	n/a
4	SETDB1	chr10:27541063-27541911	K562	blood:	n/a	n/a
5	POLR2A	chr10:27541037-27541128	H1-hESC	embryonic stem cell:	n/a	n/a
6	MAX	chr10:27541083-27541965	H1-hESC	embryonic stem cell:	n/a	n/a
7	TEAD4	chr10:27541014-27541473	H1-hESC	embryonic stem cell:	n/a	n/a
8	CTCF	chr10:27541080-27541230	HPF	lung:	n/a	n/a
9	BCLAF1	chr10:27541072-27541462	GM12878	blood:	n/a	n/a
10	MTA3	chr10:27541097-27542001	GM12878	blood:	n/a	n/a
11	POLR2A	chr10:27541030-27541965	H1-hESC	embryonic stem cell:	n/a	n/a
12	CTCF	chr10:27540980-27541130	HA-sp	spinal cord:	n/a	n/a
13	MAX	chr10:27541034-27541886	HCT-116	colon:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr10:27442115..27444569-chr10:27537853..27541412,3	K562	blood:
2	chr10:27529474..27534457-chr10:27540904..27545668,8	MCF-7	breast:
3	chr10:27529521..27534854-chr10:27538591..27544292,11	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ACBD5-1	chr10:27534782-27541235	NR_003525

No data

Variant related genes	Relation type
LRRC37A6P	TF binding region
ENSG00000136758	Chromatin interaction
ENSG00000120539	Chromatin interaction
ENSG00000262412	Chromatin interaction
ENSG00000107897	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10764674	1.00[AMR][1000 genomes]
rs10829210	1.00[AMR][1000 genomes]
rs11015569	1.00[AMR][1000 genomes]
rs1148168	1.00[AMR][1000 genomes]
rs1148170	1.00[AMR][1000 genomes]
rs1630674	1.00[AMR][1000 genomes]
rs1753410	1.00[AMR][1000 genomes]
rs1755400	1.00[AMR][1000 genomes]
rs1755402	1.00[AMR][1000 genomes]
rs1775355	1.00[AMR][1000 genomes]
rs1887824	1.00[AMR][1000 genomes]
rs2479910	1.00[AMR][1000 genomes]
rs2479913	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2479916	1.00[AMR][1000 genomes]
rs2480716	1.00[AMR][1000 genomes]
rs2480717	1.00[AMR][1000 genomes]
rs2489371	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3118890	1.00[AMR][1000 genomes]
rs4747591	1.00[AMR][1000 genomes]
rs487219	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs493598	1.00[AMR][1000 genomes]
rs525441	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs530567	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56030738	1.00[AMR][1000 genomes]
rs605028	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs605354	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs607717	1.00[AMR][1000 genomes]
rs60918938	1.00[AMR][1000 genomes]
rs641128	1.00[AMR][1000 genomes]
rs646612	1.00[AMR][1000 genomes]
rs658082	1.00[AMR][1000 genomes]
rs695044	1.00[AMR][1000 genomes]
rs7082922	1.00[AMR][1000 genomes]
rs7095372	1.00[AMR][1000 genomes]
rs788200	1.00[AMR][1000 genomes]
rs788206	1.00[AMR][1000 genomes]
rs788213	1.00[AMR][1000 genomes]
rs788217	1.00[AMR][1000 genomes]
rs788224	1.00[AMR][1000 genomes]
rs788225	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs788231	1.00[AMR][1000 genomes]
rs788233	1.00[AMR][1000 genomes]
rs788236	1.00[AMR][1000 genomes]
rs788238	1.00[AMR][1000 genomes]
rs796842	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2422253	chr10:27431366-27575370	Strong transcription Genic enhancers Active TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	esv3337781	chr10:27472216-27666703	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv8614	chr10:27504487-27828406	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
4	nsv947786	chr10:27535141-27541912	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:27532600-27541200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr10:27532600-27541200	Weak transcription	Esophagus	oesophagus
3	chr10:27532600-27541200	Weak transcription	Pancreas	Pancrea
4	chr10:27532600-27541200	Weak transcription	Rectal Smooth Muscle	rectum
5	chr10:27532800-27541200	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr10:27532800-27541200	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr10:27532800-27541200	Weak transcription	Right Ventricle	heart
8	chr10:27533000-27541200	Weak transcription	Primary T cells from cord blood	blood
9	chr10:27533000-27541200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr10:27533000-27541200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr10:27533000-27541200	Weak transcription	Brain Cingulate Gyrus	brain
12	chr10:27533000-27541200	Weak transcription	Brain Substantia Nigra	brain
13	chr10:27533000-27541200	Weak transcription	Fetal Kidney	kidney
14	chr10:27536400-27541200	Weak transcription	Fetal Intestine Large	intestine
15	chr10:27536400-27541200	Weak transcription	Fetal Intestine Small	intestine
16	chr10:27537200-27541200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr10:27537200-27541200	Weak transcription	Fetal Muscle Leg	muscle
18	chr10:27537200-27541200	Weak transcription	Right Atrium	heart
19	chr10:27537200-27541400	Weak transcription	Psoas Muscle	Psoas
20	chr10:27538000-27541200	Weak transcription	Left Ventricle	heart
21	chr10:27538000-27541200	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr10:27538000-27547200	Weak transcription	Fetal Heart	heart
23	chr10:27540400-27541200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr10:27540600-27541800	Enhancers	Spleen	Spleen
25	chr10:27541000-27541200	Enhancers	Primary T cells fromperipheralblood	blood
26	chr10:27541000-27541200	Enhancers	Primary hematopoietic stem cells	blood
27	chr10:27541000-27541200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
28	chr10:27541000-27541200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
29	chr10:27541000-27541200	Enhancers	Primary T killer memory cells from peripheral blood	blood
30	chr10:27541000-27541200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr10:27541000-27541200	Enhancers	Adipose Nuclei	Adipose
32	chr10:27541000-27541200	Enhancers	Duodenum Mucosa	Duodenum
33	chr10:27541000-27541200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
34	chr10:27541000-27541200	Enhancers	Placenta	Placenta
35	chr10:27541000-27541200	Enhancers	Fetal Thymus	thymus
36	chr10:27541000-27541200	Enhancers	Stomach Mucosa	stomach
37	chr10:27541000-27541400	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
38	chr10:27541000-27541400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
39	chr10:27541000-27541400	Enhancers	Primary B cells from peripheral blood	blood
40	chr10:27541000-27541400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
41	chr10:27541000-27541400	Flanking Active TSS	Hela-S3	cervix
42	chr10:27541000-27541400	Flanking Active TSS	K562	blood
43	chr10:27541000-27541600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
44	chr10:27541000-27541600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
45	chr10:27541000-27542200	Active TSS	Skeletal Muscle Male	skeletal muscle
46	chr10:27541000-27542400	Active TSS	ES-I3 Cell Line	embryonic stem cell
47	chr10:27541000-27542400	Active TSS	Monocytes-CD14+_RO01746	blood

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