Variant report

Variant	rs2968558
Chromosome Location	chr7:140373326-140373327
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:160)
CpG islands
(count:61)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:160 , 50 per page) page: 1 2 3 4

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr7:140372526-140373472	H1-neurons	neurons:	n/a	n/a
2	CTCF	chr7:140373320-140373470	NHEK	skin:	n/a	n/a
3	CTCF	chr7:140373280-140373430	GM06990	blood:	n/a	n/a
4	CHD2	chr7:140373165-140373347	K562	blood:	n/a	n/a
5	MAX	chr7:140372431-140373722	H1-hESC	embryonic stem cell:	n/a	chr7:140372802-140372812 chr7:140372990-140373000
6	EBF1	chr7:140373189-140373341	GM12878	blood:	n/a	chr7:140373206-140373217
7	RCOR1	chr7:140373287-140373428	K562	blood:	n/a	n/a
8	POLR2A	chr7:140372420-140373536	GM12878	blood:	n/a	n/a
9	POLR2A	chr7:140372433-140373614	HCT-116	colon:	n/a	n/a
10	POLR2A	chr7:140372586-140373645	K562	blood:	n/a	n/a
11	KAP1	chr7:140373211-140373424	U2OS	brain:	n/a	n/a
12	POLR2A	chr7:140372447-140373749	HEK293	kidney:	n/a	n/a
13	POLR2A	chr7:140372699-140373380	A549	lung:	n/a	n/a
14	UBTF	chr7:140372857-140373487	K562	blood:	n/a	n/a
15	NR2F2	chr7:140373051-140373747	K562	blood:	n/a	n/a
16	CTCF	chr7:140373300-140373450	GM06990	blood:	n/a	n/a
17	CTCF	chr7:140373320-140373470	GM12865	blood:	n/a	n/a
18	POLR2A	chr7:140372572-140373509	K562	blood:	n/a	n/a
19	CBX3	chr7:140372988-140373477	K562	blood:	n/a	n/a
20	JUND	chr7:140373090-140373562	K562	blood:	n/a	n/a
21	E2F6	chr7:140372447-140373554	K562	blood:	n/a	chr7:140372848-140372858 chr7:140372998-140373013
22	E2F4	chr7:140373003-140373561	MCF10A-Er-Src	breast:	n/a	n/a
23	CTCF	chr7:140373326-140373434	GM12892	blood:	n/a	n/a
24	MAZ	chr7:140372359-140373651	GM12878	blood:	n/a	chr7:140372802-140372812 chr7:140372990-140373000
25	CTCF	chr7:140373320-140373470	RPTEC	kidney:	n/a	n/a
26	ELF1	chr7:140372574-140374124	GM12878	blood:	n/a	chr7:140372797-140372809
27	POLR2A	chr7:140372427-140373802	MCF-7	breast:	n/a	n/a
28	CTCF	chr7:140373300-140373450	HCPEpiC	choroid plexus:	n/a	n/a
29	CTCF	chr7:140373320-140373470	HUVEC	blood vessel:	n/a	n/a
30	ZEB1	chr7:140372503-140374016	GM12878	blood:	n/a	n/a
31	POLR2A	chr7:140372684-140373425	A549	lung:	n/a	n/a
32	HEY1	chr7:140372670-140373439	K562	blood:	n/a	chr7:140372788-140372803 chr7:140372809-140372824
33	POLR2A	chr7:140372677-140373622	GM12892	blood:	n/a	n/a
34	MAZ	chr7:140372063-140373834	K562	blood:	n/a	chr7:140372802-140372812 chr7:140372990-140373000
35	POLR2A	chr7:140372665-140373748	HCT-116	colon:	n/a	n/a
36	TCF3	chr7:140372718-140373393	GM12878	blood:	n/a	n/a
37	CTCF	chr7:140373200-140373350	GM12872	blood:	n/a	n/a
38	MAX	chr7:140373003-140373791	MCF-7	breast:	n/a	n/a
39	CTCF	chr7:140373300-140373450	GM12873	blood:	n/a	n/a
40	POLR2A	chr7:140372437-140373543	GM12878	blood:	n/a	n/a
41	POLR2A	chr7:140372965-140373514	GM12892	blood:	n/a	n/a
42	NR2F2	chr7:140372507-140373810	MCF-7	breast:	n/a	n/a
43	RUNX3	chr7:140373057-140373570	GM12878	blood:	n/a	n/a
44	MAX	chr7:140372607-140373664	GM12878	blood:	n/a	chr7:140372802-140372812 chr7:140372990-140373000
45	MTA3	chr7:140372943-140374693	GM12878	blood:	n/a	n/a
46	CTCF	chr7:140373280-140373430	GM12866	blood:	n/a	n/a
47	ZBTB7A	chr7:140372495-140373469	K562	blood:	n/a	n/a
48	MYC	chr7:140372576-140373625	K562	blood:	n/a	chr7:140372802-140372812 chr7:140372990-140373000
49	MAX	chr7:140372457-140373758	MCF-7	breast:	n/a	chr7:140372802-140372812 chr7:140372990-140373000
50	TBP	chr7:140373254-140373543	H1-hESC	embryonic stem cell:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr7:140373292-140373342	IMR90	lung:	fetal
2	chr7:140373292-140373342	HIPEpiC	eye:	n/a
3	chr7:140373292-140373342	GM12891	blood:	n/a
4	chr7:140373292-140373342	NHDF-neo	bronchial:	n/a
5	chr7:140373292-140373342	BE2_C	brain:	n/a
6	chr7:140373292-140373342	PrEC	prostate:	n/a
7	chr7:140373292-140373342	HUVEC	blood vessel:	n/a
8	chr7:140373292-140373342	NHBE	bronchial:	n/a
9	chr7:140373292-140373342	ProgFib	skin:	n/a
10	chr7:140373292-140373342	AoSMC	blood vessel:	n/a
11	chr7:140373292-140373342	GM12878	blood:	n/a
12	chr7:140373292-140373342	Hela-S3	cervix:	n/a
13	chr7:140373292-140373342	AG04450	lung:	fetal
14	chr7:140373292-140373342	U87	brain:	n/a
15	chr7:140373292-140373342	HEK293	kidney:	embryo
16	chr7:140373292-140373342	CMK	blood:	n/a
17	chr7:140373292-140373342	ovcar-3	ovarian:	n/a
18	chr7:140373292-140373342	HMEC	breast:	n/a
19	chr7:140373292-140373342	NH-A	brain:	n/a
20	chr7:140373292-140373342	T-47D	breast:	n/a
21	chr7:140373292-140373342	HCPEpiC	choroid plexus:	n/a
22	chr7:140373292-140373342	HepG2	liver:	n/a
23	chr7:140373292-140373342	NB4	blood:	n/a
24	chr7:140373292-140373342	AG04449	skin:	fetal
25	chr7:140373292-140373342	HCF	heart:	n/a
26	chr7:140373292-140373342	BJ	skin:	n/a
27	chr7:140373292-140373342	GM12892	blood:	n/a
28	chr7:140373292-140373342	SK-N-SH_RA	brain:	n/a
29	chr7:140373292-140373342	Caco-2	colon:	n/a
30	chr7:140373292-140373342	HRPEpiC	eye:	n/a
31	chr7:140373292-140373342	MCF-7	breast:	n/a
32	chr7:140373292-140373342	Jurkat	blood:	n/a
33	chr7:140373292-140373342	GM19239	blood:	n/a
34	chr7:140373292-140373342	HCT-116	colon:	n/a
35	chr7:140373292-140373342	MCF10A-Er-Src	breast:	n/a
36	chr7:140373292-140373342	HEEpiC	esophagus:	n/a
37	chr7:140373292-140373342	HRCEpiC	kidney:	n/a
38	chr7:140373292-140373342	ECC-1	luminal epithelium:	n/a
39	chr7:140373292-140373342	PANC-1	pancreas:	n/a
40	chr7:140373292-140373342	SK-N-MC	brain:	n/a
41	chr7:140373292-140373342	AG09309	skin:	n/a
42	chr7:140373292-140373342	LNCaP	prostate:	n/a
43	chr7:140373292-140373342	HNPCEpiC	eye:	n/a
44	chr7:140373292-140373342	A549	lung:	n/a
45	chr7:140373292-140373342	NT2-D1	testis:	n/a
46	chr7:140373292-140373342	HAEpiC	amniotic membrane:	n/a
47	chr7:140373292-140373342	RPTEC	kidney:	n/a
48	chr7:140373292-140373342	PFSK-1	brain:	n/a
49	chr7:140373292-140373342	HL-60	blood:	n/a
50	chr7:140373292-140373342	GM06990	blood:	n/a

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

No.	Distal block	Cell Line	Cell type
1	chr7:140372637..140375611-chr7:140394231..140397834,5	K562	blood:
2	chr7:140370608..140383131-chr7:140387718..140398587,28	MCF-7	breast:
3	chr7:140372831..140374417-chr7:140400299..140402616,2	MCF-7	breast:
4	chr7:140371506..140376729-chr7:140377280..140380130,6	K562	blood:
5	chr7:140371560..140374067-chr7:140396511..140398663,2	K562	blood:
6	chr7:140371193..140374993-chr7:140376654..140380151,6	MCF-7	breast:
7	chr7:140370275..140375389-chr7:140393210..140401279,16	MCF-7	breast:

No data

Variant related genes	Relation type
ADCK2	TF binding region
ADCK2	CpG island
ENSG00000133597	Chromatin interaction
ENSG00000240889	Chromatin interaction
ENSG00000090266	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10228254	0.85[ASN][1000 genomes]
rs10258462	0.85[ASN][1000 genomes]
rs10258465	0.85[ASN][1000 genomes]
rs10260676	0.83[ASN][1000 genomes]
rs1140034	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12375245	0.81[ASN][1000 genomes]
rs17161668	0.81[ASN][1000 genomes]
rs2364393	0.85[ASN][1000 genomes]
rs2364394	0.85[ASN][1000 genomes]
rs2364395	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2364397	0.81[ASN][1000 genomes]
rs28517771	0.90[ASN][1000 genomes]
rs2907950	0.89[ASN][1000 genomes]
rs2930315	0.84[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs2930318	0.94[ASN][1000 genomes]
rs2930319	0.84[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs2930331	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2968549	0.87[ASN][1000 genomes]
rs2968550	0.87[ASN][1000 genomes]
rs2968551	0.92[ASN][1000 genomes]
rs2968553	0.84[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs2968555	0.96[ASN][1000 genomes]
rs2968559	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4624945	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4725799	0.81[ASN][1000 genomes]
rs4727011	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4727021	0.81[ASN][1000 genomes]
rs4727036	0.81[ASN][1000 genomes]
rs6464937	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6977834	0.87[ASN][1000 genomes]
rs73505645	0.90[ASN][1000 genomes]
rs73505647	0.88[ASN][1000 genomes]
rs7792746	0.88[ASN][1000 genomes]
rs7794857	0.85[ASN][1000 genomes]
rs7803697	0.87[ASN][1000 genomes]
rs7809339	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831157	chr7:140241339-140426876	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	esv3373922	chr7:140371933-140374031	Active TSS Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2968558	ADCK2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:140372000-140373400	Active TSS	Primary T helper naive cells from peripheral blood	blood
2	chr7:140372200-140373400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr7:140372200-140373400	Active TSS	Primary T killer naive cells fromperipheralblood	blood
4	chr7:140372200-140373400	Active TSS	Brain Inferior Temporal Lobe	brain
5	chr7:140372200-140373400	Active TSS	Fetal Brain Female	brain
6	chr7:140372200-140373400	Active TSS	Placenta	Placenta
7	chr7:140372200-140373400	Active TSS	Right Atrium	heart
8	chr7:140372200-140373600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr7:140372200-140373600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr7:140372200-140373600	Active TSS	Brain Angular Gyrus	brain
11	chr7:140372200-140373800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr7:140372200-140373800	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr7:140372200-140374000	Active TSS	Duodenum Smooth Muscle	Duodenum
14	chr7:140372400-140373400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr7:140372400-140373400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr7:140372400-140373400	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
17	chr7:140372400-140373400	Active TSS	Primary T killer memory cells from peripheral blood	blood
18	chr7:140372400-140373400	Active TSS	Brain Substantia Nigra	brain
19	chr7:140372400-140373400	Active TSS	Colon Smooth Muscle	Colon
20	chr7:140372400-140373400	Weak transcription	Fetal Heart	heart
21	chr7:140372400-140373400	Active TSS	Fetal Intestine Large	intestine
22	chr7:140372400-140373400	Active TSS	Fetal Stomach	stomach
23	chr7:140372400-140373400	Active TSS	Rectal Mucosa Donor 31	rectum
24	chr7:140372400-140373400	Active TSS	Right Ventricle	heart
25	chr7:140372400-140373400	Active TSS	A549	lung
26	chr7:140372400-140373600	Active TSS	HUES48 Cell Line	embryonic stem cell
27	chr7:140372400-140373600	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
28	chr7:140372400-140373600	Active TSS	iPS-15b Cell Line	embryonic stem cell
29	chr7:140372400-140373600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr7:140372400-140373600	Active TSS	Breast Myoepithelial Primary Cells	Breast
31	chr7:140372400-140373600	Active TSS	Brain Anterior Caudate	brain
32	chr7:140372400-140373600	Active TSS	Brain Cingulate Gyrus	brain
33	chr7:140372400-140373600	Active TSS	Fetal Intestine Small	intestine
34	chr7:140372400-140373600	Active TSS	Psoas Muscle	Psoas
35	chr7:140372400-140373600	Active TSS	Rectal Mucosa Donor 29	rectum
36	chr7:140372400-140373600	Active TSS	HSMM	muscle
37	chr7:140372400-140373600	Active TSS	NHDF-Ad	bronchial
38	chr7:140372400-140373600	Active TSS	NHLF	lung
39	chr7:140372400-140373800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
40	chr7:140372400-140373800	Active TSS	H9 Cell Line	embryonic stem cell
41	chr7:140372400-140373800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr7:140372400-140373800	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
43	chr7:140372400-140373800	Active TSS	Ovary	ovary
44	chr7:140372400-140374000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
45	chr7:140372400-140374000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
46	chr7:140372400-140374400	Active TSS	Pancreatic Islets	Pancreatic Islet
47	chr7:140372600-140373400	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr7:140372600-140373400	Active TSS	Primary T cells from cord blood	blood
49	chr7:140372600-140373400	Active TSS	Primary T helper naive cells fromperipheralblood	blood
50	chr7:140372600-140373400	Active TSS	Primary T helper cells PMA-I stimulated	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links