Variant report

Variant	rs4142502
Chromosome Location	chr6:143875971-143875972
allele	C/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:3)
LncRNA
region (count:8)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

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

No.	Distal block	Cell Line	Cell type
1	chr6:143856385..143859400-chr6:143873221..143878065,7	MCF-7	breast:
2	chr6:143825880..143828430-chr6:143875843..143877779,2	K562	blood:
3	chr6:143866196..143871091-chr6:143873413..143876633,4	K562	blood:

(count:8 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-FUCA2-1	chr6:143875462-143876367	ENSG00000235740.1
2	lnc-FUCA2-1	chr6:143875921-143876370	NONHSAT115358
3	lnc-FUCA2-1	chr6:143875373-143876367	NONHSAT115359
4	lnc-FUCA2-1	chr6:143875252-143876367	NR_027114
5	lnc-FUCA2-1	chr6:143875252-143876367	NR_027113
6	lnc-FUCA2-1	chr6:143875252-143876367	NR_110148
7	lnc-FUCA2-1	chr6:143875252-143876367	NR_110149
8	lnc-FUCA2-1	chr6:143875467-143876367	NONHSAT115361

No data

Variant related genes	Relation type
ENSG00000112419	Chromatin interaction
ENSG00000229036	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10457749	0.80[TSI][hapmap]
rs12190134	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12191296	0.83[EUR][1000 genomes]
rs12199016	0.84[EUR][1000 genomes]
rs12203367	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12204876	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12205130	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12208244	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12210250	0.89[EUR][1000 genomes]
rs12212759	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12216096	0.85[CEU][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17072813	0.83[CHD][hapmap]
rs17368239	0.80[TSI][hapmap]
rs2027280	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs56381834	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6919613	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs72995603	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73003366	0.82[EUR][1000 genomes]
rs7744771	0.84[EUR][1000 genomes]
rs9321924	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9484777	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9496663	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9496677	0.92[CEU][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9496703	0.83[CHD][hapmap]

No data

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:143859400-143876000	Weak transcription	Primary hematopoietic stem cells	blood
2	chr6:143865400-143877800	Weak transcription	Primary monocytes fromperipheralblood	blood
3	chr6:143865800-143876000	Weak transcription	Fetal Heart	heart
4	chr6:143866800-143904600	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr6:143867400-143876000	Weak transcription	Monocytes-CD14+_RO01746	blood
6	chr6:143867600-143876000	Enhancers	Primary T helper cells PMA-I stimulated	--
7	chr6:143868200-143883600	Weak transcription	Gastric	stomach
8	chr6:143870400-143877000	Enhancers	Fetal Intestine Small	intestine
9	chr6:143871000-143879000	Weak transcription	Duodenum Mucosa	Duodenum
10	chr6:143871200-143876200	Weak transcription	HSMM	muscle
11	chr6:143871400-143876000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr6:143871600-143876000	Weak transcription	GM12878-XiMat	blood
13	chr6:143872200-143876000	Enhancers	Primary T helper cells fromperipheralblood	blood
14	chr6:143874000-143876000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
15	chr6:143874200-143876000	Enhancers	Primary T killer memory cells from peripheral blood	blood
16	chr6:143874200-143876000	Enhancers	K562	blood
17	chr6:143874200-143877600	Enhancers	Fetal Intestine Large	intestine
18	chr6:143874600-143876000	Enhancers	Primary T cells fromperipheralblood	blood
19	chr6:143874600-143876400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
20	chr6:143875200-143888200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr6:143875400-143877600	Enhancers	Fetal Thymus	thymus
22	chr6:143875400-143878200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr6:143875600-143876000	Enhancers	Primary hematopoietic stem cells short term culture	blood
24	chr6:143875600-143876200	Enhancers	Fetal Kidney	kidney
25	chr6:143875600-143876600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr6:143875600-143876800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
27	chr6:143875600-143876800	Enhancers	Thymus	Thymus
28	chr6:143875600-143876800	Enhancers	HUVEC	blood vessel
29	chr6:143875600-143877000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr6:143875600-143877000	Enhancers	Small Intestine	intestine
31	chr6:143875600-143877000	Enhancers	Stomach Mucosa	stomach
32	chr6:143875600-143877000	Enhancers	HepG2	liver
33	chr6:143875800-143876000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
34	chr6:143875800-143876000	Enhancers	HMEC	breast
35	chr6:143875800-143876200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
36	chr6:143875800-143876200	Enhancers	NH-A	brain
37	chr6:143875800-143876400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr6:143875800-143876600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
39	chr6:143875800-143876600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
40	chr6:143875800-143876600	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr6:143875800-143876600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr6:143875800-143876600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr6:143875800-143876800	Flanking Active TSS	Primary T cells from cord blood	blood
44	chr6:143875800-143876800	Enhancers	NHEK	skin
45	chr6:143875800-143877000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
46	chr6:143875800-143877000	Active TSS	Pancreatic Islets	Pancreatic Islet
47	chr6:143875800-143877000	Enhancers	Rectal Mucosa Donor 31	rectum
48	chr6:143875800-143877600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr6:143875800-143882600	Weak transcription	Left Ventricle	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links