Variant report

Variant	rs2144165
Chromosome Location	chr6:140175154-140175155
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:61)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RFX5	chr6:140174512-140175504	IMR90	lung:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr6:140175142-140175192	AG09309	skin:	n/a
2	chr6:140175142-140175192	BJ	skin:	n/a
3	chr6:140175142-140175192	CMK	blood:	n/a
4	chr6:140175142-140175192	SK-N-MC	brain:	n/a
5	chr6:140175142-140175192	BE2_C	brain:	n/a
6	chr6:140175142-140175192	GM06990	blood:	n/a
7	chr6:140175142-140175192	HepG2	liver:	n/a
8	chr6:140175142-140175192	Hela-S3	cervix:	n/a
9	chr6:140175142-140175192	Jurkat	blood:	n/a
10	chr6:140175142-140175192	IMR90	lung:	fetal
11	chr6:140175142-140175192	NH-A	brain:	n/a
12	chr6:140175142-140175192	ECC-1	luminal epithelium:	n/a
13	chr6:140175142-140175192	ovcar-3	ovarian:	n/a
14	chr6:140175142-140175192	PrEC	prostate:	n/a
15	chr6:140175142-140175192	SK-N-SH_RA	brain:	n/a
16	chr6:140175142-140175192	Caco-2	colon:	n/a
17	chr6:140175142-140175192	T-47D	breast:	n/a
18	chr6:140175142-140175192	GM12878	blood:	n/a
19	chr6:140175142-140175192	AoSMC	blood vessel:	n/a
20	chr6:140175142-140175192	HEEpiC	esophagus:	n/a
21	chr6:140175142-140175192	SKMC	muscle:	n/a
22	chr6:140175142-140175192	HIPEpiC	eye:	n/a
23	chr6:140175142-140175192	HL-60	blood:	n/a
24	chr6:140175142-140175192	RPTEC	kidney:	n/a
25	chr6:140175142-140175192	AG04449	skin:	fetal
26	chr6:140175142-140175192	MCF10A-Er-Src	breast:	n/a
27	chr6:140175142-140175192	GM12892	blood:	n/a
28	chr6:140175142-140175192	HPAEpiC	pulmonary alveolar:	n/a
29	chr6:140175142-140175192	HCF	heart:	n/a
30	chr6:140175142-140175192	H1-hESC	embryonic stem cell:	embryo
31	chr6:140175142-140175192	Hepatocyte	liver:	n/a
32	chr6:140175142-140175192	SK-N-SH	brain:	n/a
33	chr6:140175142-140175192	HNPCEpiC	eye:	n/a
34	chr6:140175142-140175192	NT2-D1	testis:	n/a
35	chr6:140175142-140175192	HUVEC	blood vessel:	n/a
36	chr6:140175142-140175192	AG09319	gingival:	n/a
37	chr6:140175142-140175192	PANC-1	pancreas:	n/a
38	chr6:140175142-140175192	HAEpiC	amniotic membrane:	n/a
39	chr6:140175142-140175192	HCT-116	colon:	n/a
40	chr6:140175142-140175192	A549	lung:	n/a
41	chr6:140175142-140175192	SAEC	small airway:	n/a
42	chr6:140175142-140175192	GM12891	blood:	n/a
43	chr6:140175142-140175192	NHBE	bronchial:	n/a
44	chr6:140175142-140175192	AG10803	skin:	n/a
45	chr6:140175142-140175192	AG04450	lung:	fetal
46	chr6:140175142-140175192	HEK293	kidney:	embryo
47	chr6:140175142-140175192	LNCaP	prostate:	n/a
48	chr6:140175142-140175192	K562	blood:	n/a
49	chr6:140175142-140175192	ProgFib	skin:	n/a
50	chr6:140175142-140175192	HRE	kidney:	n/a

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:139694169..139695837-chr6:140173549..140176425,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000231426	TF binding region
ENSG00000231426	CpG island
ENSG00000164442	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs11963806	1.00[ASN][1000 genomes]
rs12110570	1.00[ASN][1000 genomes]
rs17811355	0.81[AMR][1000 genomes]
rs2179995	1.00[ASN][1000 genomes]
rs2179996	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2207334	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3001016	1.00[ASN][1000 genomes]
rs3015438	1.00[ASN][1000 genomes]
rs3918473	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3946063	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4403279	1.00[ASN][1000 genomes]
rs4554334	0.81[AMR][1000 genomes]
rs4896490	0.81[AMR][1000 genomes]
rs4896491	0.83[AMR][1000 genomes]
rs4896492	0.95[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs55772636	0.81[AMR][1000 genomes]
rs6570382	1.00[ASN][1000 genomes]
rs6570383	1.00[ASN][1000 genomes]
rs6900161	1.00[ASN][1000 genomes]
rs6900843	1.00[ASN][1000 genomes]
rs6912157	1.00[ASN][1000 genomes]
rs6917570	1.00[ASN][1000 genomes]
rs6917808	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6939887	1.00[ASN][1000 genomes]
rs72986790	1.00[ASN][1000 genomes]
rs73778053	0.81[AMR][1000 genomes]
rs73778057	0.81[AMR][1000 genomes]
rs73778058	0.81[AMR][1000 genomes]
rs7743495	1.00[ASN][1000 genomes]
rs7745714	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7746560	1.00[ASN][1000 genomes]
rs7750105	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7761684	1.00[ASN][1000 genomes]
rs7762012	1.00[ASN][1000 genomes]
rs7768688	1.00[ASN][1000 genomes]
rs7775904	1.00[ASN][1000 genomes]
rs9376470	1.00[ASN][1000 genomes]
rs9399296	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869066	chr6:139777114-140639695	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	26 gene(s)	inside rSNPs	diseases
2	nsv830820	chr6:140059279-140255292	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a
3	nsv1017015	chr6:140084137-140300565	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv1019407	chr6:140087307-140304334	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv1016532	chr6:140174639-141029988	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:140168800-140177000	Weak transcription	HUES48 Cell Line	embryonic stem cell
2	chr6:140169000-140177000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
3	chr6:140172200-140175200	Enhancers	Rectal Mucosa Donor 31	rectum
4	chr6:140172200-140178800	Enhancers	Fetal Intestine Small	intestine
5	chr6:140172200-140179000	Enhancers	Fetal Intestine Large	intestine
6	chr6:140173000-140175400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr6:140173200-140175400	Enhancers	Muscle Satellite Cultured Cells	--
8	chr6:140173200-140177000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr6:140173400-140175200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr6:140173400-140175200	Enhancers	Duodenum Mucosa	Duodenum
11	chr6:140173400-140175200	Enhancers	NHLF	lung
12	chr6:140173400-140175400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr6:140173400-140178600	Enhancers	Colon Smooth Muscle	Colon
14	chr6:140173400-140178600	Enhancers	Osteobl	bone
15	chr6:140173400-140180200	Enhancers	Fetal Kidney	kidney
16	chr6:140173400-140182200	Enhancers	Rectal Smooth Muscle	rectum
17	chr6:140173600-140175200	Enhancers	HepG2	liver
18	chr6:140173600-140175800	Enhancers	NHDF-Ad	bronchial
19	chr6:140173800-140175400	Enhancers	Liver	Liver
20	chr6:140173800-140176000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr6:140174600-140175200	Enhancers	Fetal Stomach	stomach
22	chr6:140174600-140175400	Enhancers	Rectal Mucosa Donor 29	rectum
23	chr6:140174600-140187000	Weak transcription	Psoas Muscle	Psoas
24	chr6:140174800-140176800	Weak transcription	NH-A	brain
25	chr6:140174800-140177000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr6:140174800-140177000	Weak transcription	HUES64 Cell Line	embryonic stem cell
27	chr6:140174800-140177000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr6:140174800-140177000	Weak transcription	Fetal Lung	lung
29	chr6:140174800-140177000	Weak transcription	Ovary	ovary
30	chr6:140174800-140177200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr6:140174800-140177200	Weak transcription	K562	blood
32	chr6:140175000-140175400	Enhancers	iPS-20b Cell Line	embryonic stem cell
33	chr6:140175000-140176400	Weak transcription	HSMM	muscle
34	chr6:140175000-140177000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links