Variant report

Variant	rs3791878
Chromosome Location	chr2:171672191-171672192
allele	A/C
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	REST	chr2:171672167-171672485	H1-hESC	embryonic stem cell:	n/a	n/a
2	RAD21	chr2:171672154-171672701	MCF-7	breast:	n/a	chr2:171672407-171672426 chr2:171672328-171672342 chr2:171672410-171672423 chr2:171672411-171672425 chr2:171672413-171672422
3	REST	chr2:171672108-171672556	GM12878	blood:	n/a	chr2:171672540-171672553
4	POLR2A	chr2:171669667-171676754	H1-neurons	neurons:	n/a	n/a
5	CBX3	chr2:171672125-171672568	K562	blood:	n/a	n/a
6	RAD21	chr2:171672167-171672703	ECC-1	luminal epithelium:	n/a	chr2:171672407-171672426 chr2:171672328-171672342 chr2:171672410-171672423 chr2:171672411-171672425 chr2:171672413-171672422
7	REST	chr2:171670030-171672638	HL-60	blood:	n/a	chr2:171671032-171671045 chr2:171670866-171670875 chr2:171672540-171672553 chr2:171670866-171670886 chr2:171670866-171670886 chr2:171670869-171670882 chr2:171670872-171670886 chr2:171670867-171670885 chr2:171670866-171670886
8	CTCF	chr2:171672132-171672616	H1-hESC	embryonic stem cell:	n/a	chr2:171672410-171672426 chr2:171672412-171672422 chr2:171672411-171672424 chr2:171672404-171672425 chr2:171672411-171672424 chr2:171672415-171672424 chr2:171672409-171672427
9	HDAC2	chr2:171672180-171672580	HepG2	liver:	n/a	n/a
10	CTCF	chr2:171672080-171672230	A549	lung:	n/a	chr2:171672131-171672140
11	CTBP2	chr2:171672114-171675650	H1-hESC	embryonic stem cell:	n/a	n/a
12	REST	chr2:171671889-171672489	H1-hESC	embryonic stem cell:	n/a	n/a
13	CTCF	chr2:171672103-171672571	A549	lung:	n/a	chr2:171672410-171672426 chr2:171672412-171672422 chr2:171672411-171672424 chr2:171672131-171672140 chr2:171672404-171672425 chr2:171672411-171672424 chr2:171672415-171672424 chr2:171672409-171672427
14	CTCF	chr2:171672186-171672496	A549	lung:	n/a	chr2:171672410-171672426 chr2:171672412-171672422 chr2:171672411-171672424 chr2:171672404-171672425 chr2:171672411-171672424 chr2:171672415-171672424 chr2:171672409-171672427
15	REST	chr2:171672135-171672551	PFSK-1	brain:	n/a	n/a
16	SIN3A	chr2:171669186-171672942	H1-hESC	embryonic stem cell:	n/a	chr2:171670866-171670879 chr2:171672333-171672342 chr2:171670871-171670885 chr2:171672540-171672553
17	TCF12	chr2:171672141-171672517	H1-hESC	embryonic stem cell:	n/a	chr2:171672338-171672345
18	BRCA1	chr2:171672141-171672547	H1-hESC	embryonic stem cell:	n/a	n/a
19	SMC3	chr2:171671972-171672814	SK-N-SH	brain:	n/a	chr2:171672411-171672425
20	SMC3	chr2:171672188-171672628	Hela-S3	cervix:	n/a	chr2:171672411-171672425
21	SMC3	chr2:171672109-171672601	HepG2	liver:	n/a	chr2:171672411-171672425
22	CTCF	chr2:171671323-171672998	SK-N-SH	brain:	n/a	chr2:171672410-171672426 chr2:171672412-171672422 chr2:171672411-171672424 chr2:171672131-171672140 chr2:171672404-171672425 chr2:171672411-171672424 chr2:171672415-171672424 chr2:171672409-171672427
23	RAD21	chr2:171672177-171672666	GM12878	blood:	n/a	chr2:171672407-171672426 chr2:171672328-171672342 chr2:171672410-171672423 chr2:171672411-171672425 chr2:171672413-171672422
24	HMGN3	chr2:171672187-171672695	K562	blood:	n/a	n/a
25	ATF2	chr2:171672094-171672593	H1-hESC	embryonic stem cell:	n/a	n/a
26	RAD21	chr2:171672089-171672815	ECC-1	luminal epithelium:	n/a	chr2:171672407-171672426 chr2:171672328-171672342 chr2:171672410-171672423 chr2:171672411-171672425 chr2:171672413-171672422
27	MAX	chr2:171672115-171672453	H1-hESC	embryonic stem cell:	n/a	n/a
28	CHD2	chr2:171671936-171672511	H1-hESC	embryonic stem cell:	n/a	n/a
29	REST	chr2:171671872-171672596	ECC-1	luminal epithelium:	n/a	chr2:171672540-171672553
30	RAD21	chr2:171672164-171672586	HepG2	liver:	n/a	chr2:171672407-171672426 chr2:171672328-171672342 chr2:171672410-171672423 chr2:171672411-171672425 chr2:171672413-171672422
31	IRF3	chr2:171672133-171672205	GM12878	blood:	n/a	n/a
32	CTCF	chr2:171672133-171672622	HepG2	liver:	n/a	chr2:171672410-171672426 chr2:171672412-171672422 chr2:171672411-171672424 chr2:171672404-171672425 chr2:171672411-171672424 chr2:171672415-171672424 chr2:171672409-171672427
33	ZBTB7A	chr2:171672171-171672658	K562	blood:	n/a	chr2:171672569-171672576
34	ZBTB7A	chr2:171672167-171673026	ECC-1	luminal epithelium:	n/a	chr2:171672569-171672576
35	REST	chr2:171672009-171672524	MCF-7	breast:	n/a	n/a
36	MAX	chr2:171672180-171672778	ECC-1	luminal epithelium:	n/a	n/a
37	REST	chr2:171672007-171672465	PFSK-1	brain:	n/a	n/a
38	RAD21	chr2:171672036-171672789	A549	lung:	n/a	chr2:171672407-171672426 chr2:171672328-171672342 chr2:171672410-171672423 chr2:171672411-171672425 chr2:171672413-171672422
39	RAD21	chr2:171672074-171672731	HepG2	liver:	n/a	chr2:171672407-171672426 chr2:171672328-171672342 chr2:171672410-171672423 chr2:171672411-171672425 chr2:171672413-171672422
40	RAD21	chr2:171671967-171672695	H1-hESC	embryonic stem cell:	n/a	chr2:171672407-171672426 chr2:171672328-171672342 chr2:171672410-171672423 chr2:171672411-171672425 chr2:171672413-171672422
41	BCLAF1	chr2:171672186-171672566	GM12878	blood:	n/a	n/a
42	NR2F2	chr2:171672171-171672982	K562	blood:	n/a	n/a
43	RAD21	chr2:171671959-171672794	SK-N-SH	brain:	n/a	chr2:171672407-171672426 chr2:171672328-171672342 chr2:171672410-171672423 chr2:171672411-171672425 chr2:171672413-171672422
44	SMC3	chr2:171672149-171672908	K562	blood:	n/a	chr2:171672411-171672425
45	YY1	chr2:171672153-171672644	HepG2	liver:	n/a	n/a
46	TCF12	chr2:171672137-171672573	H1-hESC	embryonic stem cell:	n/a	chr2:171672338-171672345
47	RAD21	chr2:171672162-171672688	HepG2	liver:	n/a	chr2:171672407-171672426 chr2:171672328-171672342 chr2:171672410-171672423 chr2:171672411-171672425 chr2:171672413-171672422
48	RAD21	chr2:171672038-171673105	HCT-116	colon:	n/a	chr2:171672407-171672426 chr2:171672328-171672342 chr2:171672410-171672423 chr2:171672411-171672425 chr2:171672413-171672422
49	CTCF	chr2:171672159-171672761	K562	blood:	n/a	chr2:171672410-171672426 chr2:171672412-171672422 chr2:171672411-171672424 chr2:171672404-171672425 chr2:171672411-171672424 chr2:171672415-171672424 chr2:171672409-171672427
50	ELF1	chr2:171672170-171672998	GM12878	blood:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr2:171672156-171672206	HPAEpiC	pulmonary alveolar:	n/a
2	chr2:171672156-171672206	GM12892	blood:	n/a
3	chr2:171672156-171672206	NHBE	bronchial:	n/a
4	chr2:171672156-171672206	Jurkat	blood:	n/a
5	chr2:171672156-171672206	HCPEpiC	choroid plexus:	n/a
6	chr2:171672156-171672206	SKMC	muscle:	n/a
7	chr2:171672156-171672206	Hela-S3	cervix:	n/a
8	chr2:171672156-171672206	BE2_C	brain:	n/a
9	chr2:171672156-171672206	HRCEpiC	kidney:	n/a
10	chr2:171672156-171672206	H1-hESC	embryonic stem cell:	embryo
11	chr2:171672156-171672206	HEK293	kidney:	embryo
12	chr2:171672156-171672206	SK-N-SH_RA	brain:	n/a
13	chr2:171672156-171672206	HNPCEpiC	eye:	n/a
14	chr2:171672156-171672206	HUVEC	blood vessel:	n/a
15	chr2:171672156-171672206	HAEpiC	amniotic membrane:	n/a
16	chr2:171672156-171672206	Hepatocyte	liver:	n/a
17	chr2:171672156-171672206	PrEC	prostate:	n/a
18	chr2:171672156-171672206	GM12891	blood:	n/a
19	chr2:171672156-171672206	GM19239	blood:	n/a
20	chr2:171672156-171672206	GM06990	blood:	n/a
21	chr2:171672156-171672206	SK-N-MC	brain:	n/a
22	chr2:171672156-171672206	PANC-1	pancreas:	n/a
23	chr2:171672156-171672206	SK-N-SH	brain:	n/a
24	chr2:171672156-171672206	BJ	skin:	n/a
25	chr2:171672156-171672206	AG09309	skin:	n/a
26	chr2:171672156-171672206	AG04449	skin:	fetal
27	chr2:171672156-171672206	AoSMC	blood vessel:	n/a
28	chr2:171672156-171672206	AG04450	lung:	fetal
29	chr2:171672156-171672206	A549	lung:	n/a
30	chr2:171672156-171672206	CMK	blood:	n/a
31	chr2:171672156-171672206	HepG2	liver:	n/a
32	chr2:171672156-171672206	K562	blood:	n/a
33	chr2:171672156-171672206	HRE	kidney:	n/a
34	chr2:171672156-171672206	NB4	blood:	n/a
35	chr2:171672156-171672206	ECC-1	luminal epithelium:	n/a
36	chr2:171672156-171672206	AG09319	gingival:	n/a
37	chr2:171672156-171672206	NH-A	brain:	n/a
38	chr2:171672156-171672206	ProgFib	skin:	n/a
39	chr2:171672156-171672206	MCF10A-Er-Src	breast:	n/a
40	chr2:171672156-171672206	NT2-D1	testis:	n/a
41	chr2:171672156-171672206	HCT-116	colon:	n/a
42	chr2:171672156-171672206	GM12878	blood:	n/a
43	chr2:171672156-171672206	HIPEpiC	eye:	n/a
44	chr2:171672156-171672206	LNCaP	prostate:	n/a
45	chr2:171672156-171672206	MCF-7	breast:	n/a
46	chr2:171672156-171672206	HRPEpiC	eye:	n/a
47	chr2:171672156-171672206	IMR90	lung:	fetal
48	chr2:171672156-171672206	RPTEC	kidney:	n/a
49	chr2:171672156-171672206	PFSK-1	brain:	n/a
50	chr2:171672156-171672206	HEEpiC	esophagus:	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:171180785..171181693-chr2:171671922..171672450,2	K562	blood:
2	chr2:171671327..171674926-chr2:171677821..171681963,4	K562	blood:
3	chr2:171669367..171672253-chr2:171672351..171673917,2	K562	blood:
4	chr2:171234154..171234994-chr2:171671884..171672456,2	MCF-7	breast:
5	chr2:171671156..171674030-chr2:171674159..171676823,3	K562	blood:

Variant related genes	Relation type
GAD1	TF binding region
GAD1	CpG island
ENSG00000235934	Chromatin interaction
ENSG00000128683	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10168078	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs10930440	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs12464863	0.81[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap]
rs1420378	0.81[CHB][hapmap];0.85[JPT][hapmap];0.81[TSI][hapmap]
rs17694708	0.85[CHB][hapmap];0.83[JPT][hapmap]
rs1894920	0.85[JPT][hapmap];1.00[YRI][hapmap]
rs1978340	1.00[CHB][hapmap];0.94[CHD][hapmap];0.92[JPT][hapmap];0.84[MEX][hapmap];0.90[TSI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2287110	0.87[CHB][hapmap];0.81[CHD][hapmap];0.81[TSI][hapmap]
rs2287111	0.81[CHB][hapmap];0.85[JPT][hapmap];0.81[TSI][hapmap]
rs2356236	0.93[EUR][1000 genomes]
rs2883888	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34137349	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35127716	0.82[AMR][1000 genomes]
rs3762553	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3762556	0.91[CEU][hapmap];0.93[EUR][1000 genomes]
rs3791871	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3791872	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4668315	0.83[CHB][hapmap];0.83[JPT][hapmap]
rs56989102	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62168446	0.82[AMR][1000 genomes]
rs62168448	0.82[AMR][1000 genomes]
rs62168454	0.99[ASN][1000 genomes]
rs6755814	0.94[CHB][hapmap];0.84[CHD][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs6759584	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs7568115	0.81[CHB][hapmap];0.85[JPT][hapmap];0.81[TSI][hapmap]
rs7600585	0.81[CHB][hapmap];0.85[JPT][hapmap];0.81[TSI][hapmap]

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	esv1806894	chr2:171651783-171679041	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv528929	chr2:171672191-171678379	Bivalent/Poised TSS Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:171669600-171672200	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
2	chr2:171669600-171673000	Bivalent/Poised TSS	Fetal Brain Female	brain
3	chr2:171669600-171675400	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
4	chr2:171670200-171676200	Bivalent/Poised TSS	Brain Germinal Matrix	brain
5	chr2:171670400-171676600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
6	chr2:171670600-171672200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr2:171670600-171672600	Weak transcription	Gastric	stomach
8	chr2:171671000-171672200	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
9	chr2:171671200-171672200	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
10	chr2:171671200-171672400	Bivalent Enhancer	Primary B cells from peripheral blood	blood
11	chr2:171671200-171672400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
12	chr2:171671200-171672400	Enhancers	Spleen	Spleen
13	chr2:171671200-171672800	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
14	chr2:171671400-171672200	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
15	chr2:171671400-171672200	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
16	chr2:171671400-171672600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
17	chr2:171671400-171675200	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr2:171671400-171675400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
19	chr2:171671600-171672200	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr2:171671600-171672200	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr2:171671600-171672400	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
22	chr2:171671600-171672400	Bivalent Enhancer	Fetal Thymus	thymus
23	chr2:171671600-171673400	Enhancers	Pancreas	Pancrea
24	chr2:171671800-171672200	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
25	chr2:171671800-171672200	Flanking Bivalent TSS/Enh	ES-UCSF4 Cell Line	embryonic stem cell
26	chr2:171671800-171672200	Bivalent Enhancer	Primary T helper naive cells fromperipheralblood	blood
27	chr2:171671800-171672200	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr2:171671800-171672200	Bivalent Enhancer	HepG2	liver
29	chr2:171671800-171672400	Bivalent Enhancer	Primary T helper naive cells from peripheral blood	blood
30	chr2:171671800-171672400	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
31	chr2:171671800-171672400	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
32	chr2:171671800-171672400	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr2:171671800-171672400	Bivalent Enhancer	Esophagus	oesophagus
34	chr2:171671800-171672400	Bivalent Enhancer	Fetal Stomach	stomach
35	chr2:171671800-171675400	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
36	chr2:171672000-171672200	Flanking Bivalent TSS/Enh	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr2:171672000-171672200	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr2:171672000-171672200	Flanking Bivalent TSS/Enh	Primary T helper memory cells from peripheral blood 2	blood
39	chr2:171672000-171672200	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
40	chr2:171672000-171672200	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
41	chr2:171672000-171672200	Bivalent Enhancer	Primary T regulatory cells fromperipheralblood	blood
42	chr2:171672000-171672200	Bivalent Enhancer	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr2:171672000-171672200	Flanking Bivalent TSS/Enh	Primary T killer memory cells from peripheral blood	blood
44	chr2:171672000-171672200	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr2:171672000-171672200	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr2:171672000-171672200	Bivalent Enhancer	Adipose Nuclei	Adipose
47	chr2:171672000-171672200	Bivalent Enhancer	Brain Angular Gyrus	brain
48	chr2:171672000-171672200	Bivalent Enhancer	Brain Cingulate Gyrus	brain
49	chr2:171672000-171672200	Bivalent Enhancer	Brain Dorsolateral Prefrontal Cortex	brain
50	chr2:171672000-171672200	Flanking Bivalent TSS/Enh	Brain Substantia Nigra	brain

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