Variant report

Variant	rs2240071
Chromosome Location	chr6:30070932-30070933
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:273)
CpG islands
(count:122)
Chromatin interactive
region (count:22)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:273 , 50 per page) page: 1 2 3 4 5 6

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CHD2	chr6:30070880-30071323	GM12878	blood:	n/a	n/a
2	RAD21	chr6:30070822-30071205	SK-N-SH_RA	brain:	n/a	n/a
3	YY1	chr6:30070783-30071287	HepG2	liver:	n/a	n/a
4	RAD21	chr6:30070810-30071409	H1-hESC	embryonic stem cell:	n/a	n/a
5	KAP1	chr6:30070758-30071326	U2OS	brain:	n/a	n/a
6	CTCF	chr6:30070880-30071030	GM12869	blood:	n/a	n/a
7	ZKSCAN1	chr6:30070865-30071125	Hela-S3	cervix:	n/a	n/a
8	RAD21	chr6:30070653-30071428	MCF-7	breast:	n/a	n/a
9	FOXP2	chr6:30070865-30071208	SK-N-MC	brain:	n/a	n/a
10	RAD21	chr6:30070729-30071414	ECC-1	luminal epithelium:	n/a	n/a
11	GABPA	chr6:30070823-30071180	H1-hESC	embryonic stem cell:	n/a	n/a
12	TEAD4	chr6:30070711-30071055	H1-hESC	embryonic stem cell:	n/a	n/a
13	ELK1	chr6:30070874-30071100	Hela-S3	cervix:	n/a	n/a
14	CTCF	chr6:30070810-30071359	IMR90	lung:	n/a	n/a
15	POLR2A	chr6:30070727-30071175	HCT-116	colon:	n/a	n/a
16	CTCF	chr6:30070920-30071070	BJ	skin:	n/a	n/a
17	CTCF	chr6:30070920-30071070	GM12864	blood:	n/a	n/a
18	CTCF	chr6:30070920-30071070	WI-38	lung:	n/a	n/a
19	SP4	chr6:30070858-30071192	H1-hESC	embryonic stem cell:	n/a	n/a
20	MAZ	chr6:30070820-30071248	K562	blood:	n/a	n/a
21	JUND	chr6:30070881-30071171	H1-hESC	embryonic stem cell:	n/a	n/a
22	SMC3	chr6:30070631-30071462	SK-N-SH	brain:	n/a	n/a
23	CTCF	chr6:30070856-30071192	GM19240	blood:	n/a	n/a
24	TBL1XR1	chr6:30070907-30071172	GM12878	blood:	n/a	n/a
25	STAT3	chr6:30070856-30071128	GM12878	blood:	n/a	n/a
26	CTCF	chr6:30070872-30071148	MCF-7	breast:	n/a	n/a
27	FOXA1	chr6:30070813-30071044	ECC-1	luminal epithelium:	n/a	n/a
28	CTCF	chr6:30070877-30071162	GM10266	blood:	n/a	n/a
29	MAX	chr6:30068086-30071338	HCT-116	colon:	n/a	chr6:30069316-30069323 chr6:30069315-30069324 chr6:30068716-30068725
30	FOXA2	chr6:30070786-30071158	HepG2	liver:	n/a	n/a
31	PAX5	chr6:30070806-30071108	GM12878	blood:	n/a	n/a
32	RAD21	chr6:30070600-30071433	HCT-116	colon:	n/a	n/a
33	MAX	chr6:30070774-30071764	H1-hESC	embryonic stem cell:	n/a	n/a
34	ELF1	chr6:30070755-30071188	HepG2	liver:	n/a	chr6:30071007-30071020
35	FOXA1	chr6:30070820-30071209	T-47D	breast:	n/a	n/a
36	RAD21	chr6:30070805-30071234	GM12878	blood:	n/a	n/a
37	FOXA1	chr6:30070827-30071167	T-47D	breast:	n/a	n/a
38	CTCF	chr6:30070853-30071182	GM12878	blood:	n/a	n/a
39	MAX	chr6:30070850-30071181	NB4	blood:	n/a	n/a
40	ELK1	chr6:30070886-30071141	GM12878	blood:	n/a	n/a
41	CTCF	chr6:30070881-30071157	Kidney_OC	kidney:	n/a	n/a
42	CTCF	chr6:30070861-30071297	GM12891	blood:	n/a	n/a
43	POLR2A	chr6:30070849-30071066	HepG2	liver:	n/a	n/a
44	EBF1	chr6:30070841-30071108	GM12878	blood:	n/a	n/a
45	SPI1	chr6:30070630-30071431	GM12878	blood:	n/a	n/a
46	MYC	chr6:30070823-30071229	K562	blood:	n/a	n/a
47	RAD21	chr6:30070846-30071197	A549	lung:	n/a	n/a
48	CTCF	chr6:30070825-30071174	SK-N-SH_RA	brain:	n/a	n/a
49	CTCF	chr6:30070693-30071444	MCF-7	breast:	n/a	n/a
50	EP300	chr6:30070871-30071079	HepG2	liver:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr6:30070886-30070936	HEEpiC	esophagus:	n/a
2	chr6:30070924-30070974	NHBE	bronchial:	n/a
3	chr6:30070886-30070936	HIPEpiC	eye:	n/a
4	chr6:30070924-30070974	SK-N-SH	brain:	n/a
5	chr6:30070924-30070974	A549	lung:	n/a
6	chr6:30070886-30070936	AG09309	skin:	n/a
7	chr6:30070924-30070974	NH-A	brain:	n/a
8	chr6:30070886-30070936	NH-A	brain:	n/a
9	chr6:30070886-30070936	HRPEpiC	eye:	n/a
10	chr6:30070924-30070974	MCF10A-Er-Src	breast:	n/a
11	chr6:30070924-30070974	HRCEpiC	kidney:	n/a
12	chr6:30070886-30070936	RPTEC	kidney:	n/a
13	chr6:30070886-30070936	NB4	blood:	n/a
14	chr6:30070924-30070974	T-47D	breast:	n/a
15	chr6:30070924-30070974	LNCaP	prostate:	n/a
16	chr6:30070924-30070974	AG09319	gingival:	n/a
17	chr6:30070924-30070974	GM12892	blood:	n/a
18	chr6:30070886-30070936	HCPEpiC	choroid plexus:	n/a
19	chr6:30070924-30070974	Hepatocyte	liver:	n/a
20	chr6:30070886-30070936	MCF-7	breast:	n/a
21	chr6:30070924-30070974	MCF-7	breast:	n/a
22	chr6:30070924-30070974	HPAEpiC	pulmonary alveolar:	n/a
23	chr6:30070886-30070936	HCT-116	colon:	n/a
24	chr6:30070924-30070974	Jurkat	blood:	n/a
25	chr6:30070886-30070936	SK-N-MC	brain:	n/a
26	chr6:30070886-30070936	HCM	heart:	n/a
27	chr6:30070924-30070974	GM12891	blood:	n/a
28	chr6:30070886-30070936	Jurkat	blood:	n/a
29	chr6:30070924-30070974	Hela-S3	cervix:	n/a
30	chr6:30070924-30070974	HRPEpiC	eye:	n/a
31	chr6:30070886-30070936	GM12878	blood:	n/a
32	chr6:30070886-30070936	AG09319	gingival:	n/a
33	chr6:30070924-30070974	NB4	blood:	n/a
34	chr6:30070924-30070974	HCF	heart:	n/a
35	chr6:30070886-30070936	ovcar-3	ovarian:	n/a
36	chr6:30070924-30070974	NT2-D1	testis:	n/a
37	chr6:30070924-30070974	CMK	blood:	n/a
38	chr6:30070924-30070974	K562	blood:	n/a
39	chr6:30070886-30070936	H1-hESC	embryonic stem cell:	embryo
40	chr6:30070924-30070974	GM12878	blood:	n/a
41	chr6:30070886-30070936	SAEC	small airway:	n/a
42	chr6:30070886-30070936	HAEpiC	amniotic membrane:	n/a
43	chr6:30070924-30070974	IMR90	lung:	fetal
44	chr6:30070886-30070936	AG04450	lung:	fetal
45	chr6:30070924-30070974	HepG2	liver:	n/a
46	chr6:30070886-30070936	GM06990	blood:	n/a
47	chr6:30070886-30070936	PrEC	prostate:	n/a
48	chr6:30070924-30070974	HCM	heart:	n/a
49	chr6:30070886-30070936	CMK	blood:	n/a
50	chr6:30070924-30070974	HEEpiC	esophagus:	n/a

(count:22 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:30070301..30072986-chr6:30097734..30100221,43	MCF-7	breast:
2	chr6:30070449..30072089-chr6:30137197..30138565,6	MCF-7	breast:
3	chr6:30039673..30045870-chr6:30065915..30071954,9	MCF-7	breast:
4	chr6:30059482..30063646-chr6:30064744..30071169,8	MCF-7	breast:
5	chr6:30070520..30071450-chr6:30137404..30138412,4	MCF-7	breast:
6	chr6:30027872..30030809-chr6:30069511..30072907,4	K562	blood:
7	chr6:30070766..30071459-chr6:30135056..30135745,2	K562	blood:
8	chr6:30070544..30071580-chr6:30137122..30138246,6	K562	blood:
9	chr6:30069516..30071040-chr6:30137847..30139463,2	MCF-7	breast:
10	chr6:30068684..30075353-chr6:30179679..30184952,7	MCF-7	breast:
11	chr6:30070180..30072059-chr6:30098450..30099535,14	K562	blood:
12	chr6:30031856..30036259-chr6:30064937..30071315,10	MCF-7	breast:
13	chr6:30027986..30030809-chr6:30067690..30071011,4	K562	blood:
14	chr6:30028086..30030535-chr6:30068315..30071049,3	MCF-7	breast:
15	chr6:30043377..30045110-chr6:30070275..30072110,2	MCF-7	breast:
16	chr6:30070612..30071430-chr6:30098763..30099444,2	MCF-7	breast:
17	chr6:30042922..30044278-chr6:30069878..30071198,4	MCF-7	breast:
18	chr6:30070557..30071542-chr6:30364602..30365386,4	K562	blood:
19	chr6:30070471..30072023-chr6:30098513..30099477,20	MCF-7	breast:
20	chr6:30054838..30057804-chr6:30069131..30071158,2	MCF-7	breast:
21	chr6:29944151..29946628-chr6:30070054..30072125,2	K562	blood:
22	chr6:30043630..30044186-chr6:30070514..30071040,2	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TRIM31-1	chr6:30070674-30071022	NONHSAT108598

No data

Variant related genes	Relation type
TRIM31-AS1	TF binding region
TRIM31-AS1	CpG island
ENSG00000204619	Chromatin interaction
ENSG00000252901	Chromatin interaction
ENSG00000234127	Chromatin interaction
ENSG00000204610	Chromatin interaction
ENSG00000066379	Chromatin interaction
ENSG00000204625	Chromatin interaction
ENSG00000204618	Chromatin interaction
ENSG00000204623	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs1108052	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1108053	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1110446	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1110448	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1264694	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1264695	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1264696	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1264702	0.86[AMR][1000 genomes]
rs2072110	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2248289	0.81[EUR][1000 genomes]
rs2523994	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2524005	0.95[CEU][hapmap];0.82[CHB][hapmap];0.80[JPT][hapmap]
rs2844796	0.81[EUR][1000 genomes]
rs6457149	0.83[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs916569	0.88[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs916570	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv432866	chr6:30026321-30080921	Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	nsv884051	chr6:30059451-30071279	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv884050	chr6:30059451-30071330	Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2240071	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL
rs2240071	ZFP57	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30068000-30072600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
2	chr6:30068200-30071800	Flanking Active TSS	NHEK	skin
3	chr6:30068400-30071200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr6:30068600-30071600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
5	chr6:30069000-30071800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
6	chr6:30069400-30071000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
7	chr6:30069400-30071000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
8	chr6:30069400-30071000	Flanking Active TSS	Osteobl	bone
9	chr6:30069400-30071400	Active TSS	Esophagus	oesophagus
10	chr6:30069400-30071600	Flanking Bivalent TSS/Enh	Primary neutrophils fromperipheralblood	blood
11	chr6:30069400-30071800	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
12	chr6:30069600-30071000	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
13	chr6:30069600-30071200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr6:30069600-30071200	Active TSS	Duodenum Smooth Muscle	Duodenum
15	chr6:30069600-30071400	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
16	chr6:30069600-30071400	Active TSS	Psoas Muscle	Psoas
17	chr6:30069600-30071600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
18	chr6:30069800-30071000	Enhancers	Stomach Mucosa	stomach
19	chr6:30069800-30071000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
20	chr6:30069800-30071200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
21	chr6:30069800-30071200	Active TSS	Brain Anterior Caudate	brain
22	chr6:30069800-30071200	Active TSS	Brain Substantia Nigra	brain
23	chr6:30069800-30071200	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr6:30069800-30071800	Active TSS	Rectal Smooth Muscle	rectum
25	chr6:30070000-30071000	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
26	chr6:30070000-30071000	Bivalent Enhancer	Primary B cells from cord blood	blood
27	chr6:30070000-30071000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
28	chr6:30070000-30071000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
29	chr6:30070000-30071200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
30	chr6:30070000-30071600	Flanking Active TSS	K562	blood
31	chr6:30070000-30071800	Enhancers	Spleen	Spleen
32	chr6:30070000-30075400	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr6:30070200-30071000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr6:30070200-30071000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
35	chr6:30070200-30071000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
36	chr6:30070200-30071000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr6:30070200-30071000	Weak transcription	Aorta	Aorta
38	chr6:30070200-30071000	Flanking Active TSS	Brain Hippocampus Middle	brain
39	chr6:30070200-30071000	Enhancers	Placenta	Placenta
40	chr6:30070200-30071000	Bivalent Enhancer	Fetal Stomach	stomach
41	chr6:30070200-30071000	Bivalent Enhancer	Fetal Thymus	thymus
42	chr6:30070200-30071000	Weak transcription	Gastric	stomach
43	chr6:30070200-30071000	Weak transcription	Ovary	ovary
44	chr6:30070200-30071000	Enhancers	Pancreas	Pancrea
45	chr6:30070200-30071000	Enhancers	HMEC	breast
46	chr6:30070200-30071000	Enhancers	HSMM	muscle
47	chr6:30070200-30071000	Enhancers	HSMMtube	muscle
48	chr6:30070200-30071000	Enhancers	NHDF-Ad	bronchial
49	chr6:30070200-30071200	Active TSS	Right Ventricle	heart
50	chr6:30070200-30071400	Flanking Active TSS	Hela-S3	cervix

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