Variant report

Variant	rs971207
Chromosome Location	chr2:128181518-128181519
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:28)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:28 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr2:128181420-128181570	HAc	cerebellar:	n/a	n/a
2	CTCF	chr2:128181480-128181630	HA-sp	spinal cord:	n/a	n/a
3	CTCF	chr2:128181501-128181668	IMR90	lung:	n/a	n/a
4	CTCF	chr2:128181400-128181550	HAc	cerebellar:	n/a	n/a
5	CTCF	chr2:128181500-128181650	SK-N-SH_RA	brain:	n/a	n/a
6	CTCF	chr2:128181480-128181630	HPAF	blood vessel:	n/a	n/a
7	MXI1	chr2:128181067-128181723	IMR90	lung:	n/a	n/a
8	RFX5	chr2:128181146-128181522	Hela-S3	cervix:	n/a	n/a
9	RAD21	chr2:128181500-128181631	IMR90	lung:	n/a	n/a
10	MAX	chr2:128181152-128181550	Hela-S3	cervix:	n/a	n/a
11	TBP	chr2:128181174-128181531	Hela-S3	cervix:	n/a	n/a
12	CTCF	chr2:128181500-128181650	AG09319	gingival:	n/a	n/a
13	E2F6	chr2:128180747-128181555	A549	lung:	n/a	chr2:128181173-128181187
14	MAX	chr2:128180353-128181649	A549	lung:	n/a	n/a
15	CTCF	chr2:128181500-128181650	BJ	skin:	n/a	n/a
16	CTCF	chr2:128181380-128181530	HRE	kidney:	n/a	n/a
17	MXI1	chr2:128181114-128181599	Hela-S3	cervix:	n/a	n/a
18	MYC	chr2:128181449-128181561	MCF10A-Er-Src	breast:	n/a	n/a
19	CTCF	chr2:128181458-128181708	K562	blood:	n/a	n/a
20	CTCF	chr2:128181420-128181570	AG04450	lung:	n/a	n/a
21	JUN	chr2:128181376-128181519	H1-hESC	embryonic stem cell:	n/a	n/a
22	CTCF	chr2:128181500-128181650	RPTEC	kidney:	n/a	n/a
23	MAX	chr2:128180408-128181581	A549	lung:	n/a	n/a
24	CTCF	chr2:128181500-128181650	HMF	breast:	n/a	n/a
25	CTCF	chr2:128181480-128181630	AoAF	blood vessel:	n/a	n/a
26	SIN3A	chr2:128180348-128181579	H1-hESC	embryonic stem cell:	n/a	chr2:128181168-128181181 chr2:128181165-128181174 chr2:128180407-128180418
27	CTCF	chr2:128181460-128181610	K562	blood:	n/a	n/a
28	MXI1	chr2:128181207-128181547	H1-hESC	embryonic stem cell:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:128143986..128147167-chr2:128178825..128181533,4	MCF-7	breast:
2	chr2:128143841..128146885-chr2:128179410..128184717,5	MCF-7	breast:

No data

Variant related genes	Relation type
MIR4783	TF binding region
ENSG00000169967	Chromatin interaction
ENSG00000236682	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs12151780	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12463538	0.84[ASN][1000 genomes]
rs12464295	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12468304	0.90[ASN][1000 genomes]
rs12476767	0.84[ASN][1000 genomes]
rs12478656	0.84[ASN][1000 genomes]
rs12989081	0.83[EUR][1000 genomes]
rs13001648	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1401296	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1518759	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1799808	0.94[ASN][1000 genomes]
rs1967425	0.90[ASN][1000 genomes]
rs2069912	0.96[ASN][1000 genomes]
rs2069914	0.96[ASN][1000 genomes]
rs2069915	0.94[ASN][1000 genomes]
rs2069920	0.99[ASN][1000 genomes]
rs2069921	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2069924	0.92[ASN][1000 genomes]
rs2069931	0.90[ASN][1000 genomes]
rs2069933	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4662729	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4662730	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs5936	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62160290	0.80[ASN][1000 genomes]
rs6710535	0.90[ASN][1000 genomes]
rs6728362	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6749002	0.84[ASN][1000 genomes]
rs6754772	0.86[ASN][1000 genomes]
rs6754999	0.86[ASN][1000 genomes]
rs973760	0.87[AMR][1000 genomes];1.00[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	nsv583036	chr2:128173819-128183914	Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
2	nsv875013	chr2:128177974-128183145	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Weak transcription Bivalent Enhancer Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region miRNA	4 gene(s)	inside rSNPs	diseases
3	nsv875014	chr2:128178415-128328375	Strong transcription Flanking Bivalent TSS/Enh Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs971207	AC068282.3	cis	lung	GTEx
rs971207	AC068282.3	cis	Whole Blood	GTEx
rs971207	AC068282.3	cis	Artery Tibial	GTEx
rs971207	AC068282.3	cis	Esophagus Muscularis	GTEx
rs971207	AC068282.3	cis	Adipose Subcutaneous	GTEx
rs971207	AC068282.3	cis	Muscle Skeletal	GTEx
rs971207	AC068282.3	cis	Thyroid	GTEx
rs971207	AC068282.3	cis	Heart Left Ventricle	GTEx
rs971207	AC068282.3	cis	Stomach	GTEx

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:128180000-128181600	Weak transcription	HepG2	liver
2	chr2:128180000-128181800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
3	chr2:128180200-128181600	Active TSS	H9 Cell Line	embryonic stem cell
4	chr2:128180200-128181600	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
5	chr2:128180200-128181800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
6	chr2:128180200-128186800	Strong transcription	Liver	Liver
7	chr2:128180400-128181600	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
8	chr2:128180400-128181600	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
9	chr2:128180400-128181600	Flanking Active TSS	Primary B cells from cord blood	blood
10	chr2:128180400-128181600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
11	chr2:128180400-128181600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr2:128180400-128181600	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr2:128180400-128181600	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr2:128180400-128181800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
15	chr2:128180600-128181600	Active TSS	A549	lung
16	chr2:128180600-128181800	Active TSS	Pancreatic Islets	Pancreatic Islet
17	chr2:128180800-128181600	Bivalent/Poised TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr2:128180800-128181600	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
19	chr2:128181000-128181600	Flanking Bivalent TSS/Enh	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr2:128181000-128181600	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr2:128181000-128181600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
22	chr2:128181000-128181600	Flanking Active TSS	Primary hematopoietic stem cells	blood
23	chr2:128181000-128181600	Flanking Active TSS	Duodenum Mucosa	Duodenum
24	chr2:128181000-128181600	Active TSS	Rectal Smooth Muscle	rectum
25	chr2:128181000-128181600	Active TSS	Hela-S3	cervix
26	chr2:128181000-128181600	Flanking Bivalent TSS/Enh	HUVEC	blood vessel
27	chr2:128181000-128191000	Weak transcription	Aorta	Aorta
28	chr2:128181200-128181600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
29	chr2:128181200-128181600	Flanking Active TSS	Brain Anterior Caudate	brain
30	chr2:128181200-128181600	Bivalent Enhancer	Dnd41	blood
31	chr2:128181200-128181800	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
32	chr2:128181400-128181600	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
33	chr2:128181400-128181600	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr2:128181400-128181600	Bivalent Enhancer	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr2:128181400-128181600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr2:128181400-128181600	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
37	chr2:128181400-128181600	Bivalent Enhancer	Primary B cells from peripheral blood	blood
38	chr2:128181400-128181600	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
39	chr2:128181400-128181600	Bivalent Enhancer	Primary T regulatory cells fromperipheralblood	blood
40	chr2:128181400-128181600	Bivalent Enhancer	Primary T killer memory cells from peripheral blood	blood
41	chr2:128181400-128181600	Bivalent/Poised TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr2:128181400-128181600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr2:128181400-128181600	Active TSS	Muscle Satellite Cultured Cells	--
44	chr2:128181400-128181600	Bivalent/Poised TSS	Cortex derived primary cultured neurospheres	brain
45	chr2:128181400-128181600	Bivalent/Poised TSS	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr2:128181400-128181600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr2:128181400-128181600	Bivalent Enhancer	Adipose Nuclei	Adipose
48	chr2:128181400-128181600	Bivalent Enhancer	Brain Cingulate Gyrus	brain
49	chr2:128181400-128181600	Bivalent Enhancer	Duodenum Smooth Muscle	Duodenum
50	chr2:128181400-128181600	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links