Variant report

Variant	rs62175800
Chromosome Location	chr2:173940620-173940621
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RELA	chr2:173940245-173942075	GM12891	blood:	n/a	n/a
2	FOXA2	chr2:173940194-173940841	A549	lung:	n/a	n/a
3	POLR2A	chr2:173940248-173941962	GM18505	blood:	n/a	n/a
4	ELF1	chr2:173940266-173941637	GM12878	blood:	n/a	chr2:173940752-173940764 chr2:173940448-173940460 chr2:173941048-173941060
5	POLR2A	chr2:173940403-173941476	HUVEC	blood vessel:	n/a	n/a
6	MAX	chr2:173940408-173940776	GM12878	blood:	n/a	chr2:173940764-173940774
7	CTCF	chr2:173940480-173940630	HepG2	liver:	n/a	n/a
8	RAD21	chr2:173940385-173940760	Hela-S3	cervix:	n/a	n/a
9	SIN3AK20	chr2:173940446-173940721	PFSK-1	brain:	n/a	n/a
10	TBP	chr2:173940609-173941053	HepG2	liver:	n/a	n/a
11	MYC	chr2:173940396-173941567	MCF10A-Er-Src	breast:	n/a	chr2:173940764-173940774
12	E2F4	chr2:173940508-173940679	GM12878	blood:	n/a	chr2:173940530-173940537 chr2:173940528-173940539 chr2:173940529-173940538 chr2:173940530-173940537 chr2:173940530-173940537
13	POLR2A	chr2:173940291-173940827	U87	brain:	n/a	n/a
14	SIN3AK20	chr2:173940439-173940709	HepG2	liver:	n/a	n/a
15	POLR2A	chr2:173940313-173941698	GM19193	blood:	n/a	n/a
16	CTCF	chr2:173940520-173940670	HCT-116	colon:	n/a	n/a
17	RFX5	chr2:173940457-173940748	Hela-S3	cervix:	n/a	chr2:173940552-173940567
18	CTCF	chr2:173940445-173940632	Medullo	brain:	n/a	n/a
19	CTCF	chr2:173940500-173940650	GM06990	blood:	n/a	n/a
20	CTCF	chr2:173940520-173940670	AG04450	lung:	n/a	n/a
21	MAZ	chr2:173940089-173941626	K562	blood:	n/a	chr2:173940764-173940774
22	CHD1	chr2:173939685-173944195	IMR90	lung:	n/a	chr2:173940491-173940501 chr2:173940771-173940781 chr2:173940428-173940438 chr2:173940352-173940362
23	POLR2A	chr2:173940413-173940821	H1-neurons	neurons:	n/a	n/a
24	FOXA1	chr2:173940438-173941033	HepG2	liver:	n/a	n/a
25	CTCF	chr2:173940418-173940633	K562	blood:	n/a	n/a
26	HEY1	chr2:173940402-173941572	HepG2	liver:	n/a	chr2:173940821-173940836 chr2:173940488-173940503 chr2:173940445-173940460
27	CTCF	chr2:173940500-173940650	HFF	foreskin:	n/a	n/a
28	CTCF	chr2:173940405-173940701	A549	lung:	n/a	n/a
29	ELF1	chr2:173940325-173940887	K562	blood:	n/a	chr2:173940752-173940764 chr2:173940448-173940460
30	MYC	chr2:173940489-173940631	K562	blood:	n/a	n/a
31	TAF1	chr2:173940458-173940681	PFSK-1	brain:	n/a	n/a
32	MAX	chr2:173940034-173940826	H1-hESC	embryonic stem cell:	n/a	chr2:173940764-173940774
33	CTCF	chr2:173940404-173940713	HepG2	liver:	n/a	n/a
34	CTCF	chr2:173940500-173940650	HCFaa	heart:	n/a	n/a
35	GTF2F1	chr2:173940532-173940732	K562	blood:	n/a	n/a
36	POLR2A	chr2:173940366-173941649	Hela-S3	cervix:	n/a	n/a
37	RAD21	chr2:173940329-173941057	H1-hESC	embryonic stem cell:	n/a	chr2:173940860-173940873
38	MAX	chr2:173940257-173941448	ECC-1	luminal epithelium:	n/a	chr2:173940764-173940774
39	SMC3	chr2:173940360-173941958	Hela-S3	cervix:	n/a	chr2:173941334-173941342 chr2:173941035-173941045
40	POLR2A	chr2:173940247-173940862	U87	brain:	n/a	n/a
41	CTCFL	chr2:173940466-173940668	K562	blood:	n/a	n/a
42	TBL1XR1	chr2:173940443-173940748	K562	blood:	n/a	n/a
43	CTCF	chr2:173940400-173940711	GM19238	blood:	n/a	n/a
44	MAZ	chr2:173940333-173941429	HepG2	liver:	n/a	chr2:173940764-173940774
45	MYC	chr2:173940280-173941460	NB4	blood:	n/a	chr2:173940764-173940774
46	CTCF	chr2:173940500-173940650	GM12866	blood:	n/a	n/a
47	POLR2A	chr2:173940370-173941277	A549	lung:	n/a	n/a
48	MAX	chr2:173940169-173941826	HepG2	liver:	n/a	chr2:173940764-173940774
49	YY1	chr2:173940252-173941393	GM12878	blood:	n/a	chr2:173940978-173940987 chr2:173940973-173940987 chr2:173941041-173941055 chr2:173940447-173940461 chr2:173940973-173940982 chr2:173941035-173941049
50	POLR2A	chr2:173939908-173942230	PANC-1	pancreas:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr2:173940582-173940632	HPAEpiC	pulmonary alveolar:	n/a
2	chr2:173940582-173940632	ovcar-3	ovarian:	n/a
3	chr2:173940582-173940632	H1-hESC	embryonic stem cell:	embryo
4	chr2:173940582-173940632	ECC-1	luminal epithelium:	n/a
5	chr2:173940582-173940632	SK-N-MC	brain:	n/a
6	chr2:173940582-173940632	HCT-116	colon:	n/a
7	chr2:173940582-173940632	Hepatocyte	liver:	n/a
8	chr2:173940582-173940632	K562	blood:	n/a
9	chr2:173940582-173940632	HAEpiC	amniotic membrane:	n/a
10	chr2:173940582-173940632	MCF-7	breast:	n/a
11	chr2:173940582-173940632	BE2_C	brain:	n/a
12	chr2:173940582-173940632	GM12878	blood:	n/a
13	chr2:173940582-173940632	HepG2	liver:	n/a
14	chr2:173940582-173940632	CMK	blood:	n/a
15	chr2:173940582-173940632	HL-60	blood:	n/a
16	chr2:173940582-173940632	HIPEpiC	eye:	n/a
17	chr2:173940582-173940632	HEEpiC	esophagus:	n/a
18	chr2:173940582-173940632	A549	lung:	n/a
19	chr2:173940582-173940632	PrEC	prostate:	n/a
20	chr2:173940582-173940632	IMR90	lung:	fetal
21	chr2:173940582-173940632	HRCEpiC	kidney:	n/a
22	chr2:173940582-173940632	HMEC	breast:	n/a
23	chr2:173940582-173940632	NB4	blood:	n/a
24	chr2:173940582-173940632	HCPEpiC	choroid plexus:	n/a
25	chr2:173940582-173940632	PANC-1	pancreas:	n/a
26	chr2:173940582-173940632	AG09309	skin:	n/a
27	chr2:173940582-173940632	BJ	skin:	n/a
28	chr2:173940582-173940632	Jurkat	blood:	n/a
29	chr2:173940582-173940632	AG09319	gingival:	n/a
30	chr2:173940582-173940632	AG04450	lung:	fetal
31	chr2:173940582-173940632	GM12891	blood:	n/a
32	chr2:173940582-173940632	SK-N-SH_RA	brain:	n/a
33	chr2:173940582-173940632	HEK293	kidney:	embryo
34	chr2:173940582-173940632	NH-A	brain:	n/a
35	chr2:173940582-173940632	GM12892	blood:	n/a
36	chr2:173940582-173940632	LNCaP	prostate:	n/a
37	chr2:173940582-173940632	GM19239	blood:	n/a
38	chr2:173940582-173940632	PFSK-1	brain:	n/a
39	chr2:173940582-173940632	HNPCEpiC	eye:	n/a
40	chr2:173940582-173940632	U87	brain:	n/a
41	chr2:173940582-173940632	T-47D	breast:	n/a
42	chr2:173940582-173940632	AG10803	skin:	n/a
43	chr2:173940582-173940632	AG04449	skin:	fetal
44	chr2:173940582-173940632	GM06990	blood:	n/a
45	chr2:173940582-173940632	NHDF-neo	bronchial:	n/a
46	chr2:173940582-173940632	MCF10A-Er-Src	breast:	n/a
47	chr2:173940582-173940632	Hela-S3	cervix:	n/a
48	chr2:173940582-173940632	SAEC	small airway:	n/a
49	chr2:173940582-173940632	NT2-D1	testis:	n/a
50	chr2:173940582-173940632	SKMC	muscle:	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:173939442..173941828-chr2:174218952..174221644,4	K562	blood:
2	chr2:173939873..173942564-chr2:174828139..174830300,2	K562	blood:
3	chr19:41119049..41119660-chr2:173940484..173941219,2	HCT-116	colon:
4	chr2:173939516..173941828-chr2:174218952..174221644,5	K562	blood:
5	chr2:173925105..173930317-chr2:173940081..173942061,4	MCF-7	breast:
6	chr2:173939725..173941702-chr2:174219358..174221001,2	MCF-7	breast:
7	chr2:173939894..173941691-chr2:174070697..174073381,2	K562	blood:
8	chr2:173907898..173920360-chr2:173936226..173946823,30	MCF-7	breast:

Variant related genes	Relation type
ENSG00000091436	TF binding region
ENSG00000091436	CpG island
ENSG00000091428	Chromatin interaction
ENSG00000238133	Chromatin interaction
ENSG00000172845	Chromatin interaction
ENSG00000236391	Chromatin interaction
ENSG00000090006	Chromatin interaction
ENSG00000144354	Chromatin interaction
ENSG00000265709	Chromatin interaction

Extended variants
information (count: 5 )
Associated
traits (count: 0)

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	nsv1011724	chr2:173916482-174231908	Enhancers Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
2	nsv834460	chr2:173919464-174085288	Strong transcription Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	esv3371931	chr2:173938506-173943004	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
4	esv3410281	chr2:173939731-173942579	Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Weak transcription	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
5	esv3422715	chr2:173940006-173942054	Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:173940000-173941800	Active TSS	H1 Cell Line	embryonic stem cell
2	chr2:173940000-173941800	Active TSS	H9 Cell Line	embryonic stem cell
3	chr2:173940000-173941800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr2:173940000-173941800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr2:173940000-173941800	Active TSS	HUES6 Cell Line	embryonic stem cell
6	chr2:173940000-173941800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr2:173940000-173941800	Active TSS	NH-A	brain
8	chr2:173940000-173942000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
9	chr2:173940000-173942000	Flanking Active TSS	Primary hematopoietic stem cells	blood
10	chr2:173940000-173942000	Active TSS	Brain Angular Gyrus	brain
11	chr2:173940000-173942000	Active TSS	Brain Inferior Temporal Lobe	brain
12	chr2:173940000-173942000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
13	chr2:173940000-173942200	Active TSS	ES-I3 Cell Line	embryonic stem cell
14	chr2:173940000-173942200	Active TSS	Brain Anterior Caudate	brain
15	chr2:173940000-173942200	Active TSS	HSMMtube	muscle
16	chr2:173940000-173942600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr2:173940000-173942600	Active TSS	Aorta	Aorta
18	chr2:173940000-173942800	Active TSS	Brain Substantia Nigra	brain
19	chr2:173940000-173942800	Active TSS	Ovary	ovary
20	chr2:173940000-173943400	Active TSS	Duodenum Smooth Muscle	Duodenum
21	chr2:173940200-173941000	Active TSS	iPS-15b Cell Line	embryonic stem cell
22	chr2:173940200-173941000	Bivalent/Poised TSS	Primary T regulatory cells fromperipheralblood	blood
23	chr2:173940200-173941200	Active TSS	Primary T killer naive cells fromperipheralblood	blood
24	chr2:173940200-173941200	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
25	chr2:173940200-173941200	Active TSS	Brain Cingulate Gyrus	brain
26	chr2:173940200-173941200	Active TSS	Pancreatic Islets	Pancreatic Islet
27	chr2:173940200-173941400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
28	chr2:173940200-173941400	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
29	chr2:173940200-173941600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr2:173940200-173941600	Active TSS	Gastric	stomach
31	chr2:173940200-173941600	Active TSS	Lung	lung
32	chr2:173940200-173941600	Active TSS	Spleen	Spleen
33	chr2:173940200-173941800	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr2:173940200-173941800	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr2:173940200-173941800	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr2:173940200-173941800	Active TSS	Primary T helper naive cells fromperipheralblood	blood
37	chr2:173940200-173941800	Active TSS	Fetal Kidney	kidney
38	chr2:173940200-173941800	Active TSS	Fetal Lung	lung
39	chr2:173940200-173941800	Active TSS	Rectal Mucosa Donor 29	rectum
40	chr2:173940200-173941800	Bivalent/Poised TSS	HepG2	liver
41	chr2:173940200-173942000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
42	chr2:173940200-173942000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr2:173940200-173942000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr2:173940200-173942000	Active TSS	Colonic Mucosa	Colon
45	chr2:173940200-173942000	Active TSS	Esophagus	oesophagus
46	chr2:173940200-173942000	Active TSS	Left Ventricle	heart
47	chr2:173940200-173942000	Active TSS	Sigmoid Colon	Sigmoid Colon
48	chr2:173940200-173942000	Active TSS	Small Intestine	intestine
49	chr2:173940200-173942000	Active TSS	Stomach Mucosa	stomach
50	chr2:173940200-173942200	Active TSS	Primary T cells from cord blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links