Variant report

Variant	rs1245070
Chromosome Location	chr1:70033837-70033838
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	UBTF	chr1:70033810-70034405	K562	blood:	n/a	n/a
2	REST	chr1:70032603-70036648	H1-neurons	neurons:	n/a	chr1:70034458-70034468 chr1:70033549-70033562 chr1:70034350-70034363
3	POLR2A	chr1:70032619-70036444	H1-neurons	neurons:	n/a	n/a
4	POLR2A	chr1:70032548-70036420	H1-neurons	neurons:	n/a	n/a
5	MAX	chr1:70032684-70034559	H1-hESC	embryonic stem cell:	n/a	chr1:70033546-70033556 chr1:70032967-70032977
6	ZNF143	chr1:70033837-70034013	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr1:70033596-70033889	K562	blood:	n/a	n/a
8	SUZ12	chr1:70033449-70034240	H1-hESC	embryonic stem cell:	n/a	n/a
9	HMGN3	chr1:70033594-70034193	K562	blood:	n/a	n/a
10	GATA2	chr1:70032821-70034175	SH-SY5Y	brain:	n/a	chr1:70034157-70034168
11	E2F6	chr1:70032786-70034712	K562	blood:	n/a	chr1:70033548-70033557 chr1:70032967-70032976 chr1:70033933-70033945 chr1:70034421-70034430 chr1:70034050-70034059 chr1:70034309-70034321 chr1:70033548-70033560 chr1:70033933-70033942
12	ZNF263	chr1:70032639-70035829	HEK293-T-REx	kidney:	n/a	n/a
13	E2F6	chr1:70032779-70034603	H1-hESC	embryonic stem cell:	n/a	chr1:70033548-70033557 chr1:70032967-70032976 chr1:70033933-70033945 chr1:70034421-70034430 chr1:70034050-70034059 chr1:70034309-70034321 chr1:70033548-70033560 chr1:70033933-70033942
14	BACH1	chr1:70033759-70034415	H1-hESC	embryonic stem cell:	n/a	n/a
15	CCNT2	chr1:70033545-70034194	K562	blood:	n/a	chr1:70033548-70033557 chr1:70033933-70033942
16	SUZ12	chr1:70033600-70036320	NT2-D1	testis:	n/a	n/a
17	POLR2A	chr1:70033251-70033916	PFSK-1	brain:	n/a	n/a
18	MAX	chr1:70032966-70034046	ECC-1	luminal epithelium:	n/a	chr1:70033546-70033556 chr1:70032967-70032977
19	REST	chr1:70032593-70034195	H1-neurons	neurons:	n/a	chr1:70033549-70033562
20	CTCF	chr1:70033740-70033890	SK-N-SH_RA	brain:	n/a	n/a
21	MAX	chr1:70032701-70033892	H1-hESC	embryonic stem cell:	n/a	chr1:70033546-70033556 chr1:70032967-70032977
22	EGR1	chr1:70033420-70034096	K562	blood:	n/a	chr1:70033543-70033556 chr1:70033543-70033556 chr1:70033542-70033557
23	ZBTB7A	chr1:70033688-70033853	K562	blood:	n/a	n/a
24	TAF1	chr1:70032658-70034444	H1-neurons	neurons:	n/a	n/a
25	E2F6	chr1:70032816-70035598	H1-hESC	embryonic stem cell:	n/a	chr1:70033548-70033557 chr1:70032967-70032976 chr1:70033933-70033945 chr1:70034421-70034430 chr1:70034050-70034059 chr1:70034309-70034321 chr1:70035268-70035277 chr1:70033548-70033560 chr1:70033933-70033942
26	MAX	chr1:70033541-70034846	K562	blood:	n/a	chr1:70033546-70033556
27	MAX	chr1:70032949-70034065	ECC-1	luminal epithelium:	n/a	chr1:70033546-70033556 chr1:70032967-70032977

Variant related genes	Relation type
LRRC7	TF binding region

Extended variants
information (count: 144 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:141)

rs_ID	r²[population]
rs1012785	0.80[ASN][1000 genomes]
rs1012786	0.80[ASN][1000 genomes]
rs1014882	0.80[ASN][1000 genomes]
rs1065629	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.85[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1145922	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs1145923	0.86[ASN][1000 genomes]
rs1145924	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs1145925	0.80[ASN][1000 genomes]
rs1145926	0.80[ASN][1000 genomes]
rs1145927	0.80[ASN][1000 genomes]
rs1145928	0.80[ASN][1000 genomes]
rs1145929	0.80[ASN][1000 genomes]
rs1145930	0.80[ASN][1000 genomes]
rs1145931	0.80[ASN][1000 genomes]
rs1154974	0.86[ASN][1000 genomes]
rs1245039	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1245040	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1245043	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1245045	1.00[ASN][1000 genomes]
rs1245046	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1245047	0.86[ASW][hapmap];0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.86[MKK][hapmap];0.80[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs1245049	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.80[TSI][hapmap];1.00[ASN][1000 genomes]
rs1245050	1.00[ASN][1000 genomes]
rs1245051	0.87[ASN][1000 genomes]
rs1245052	1.00[ASN][1000 genomes]
rs1245053	1.00[JPT][hapmap]
rs1245054	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.80[TSI][hapmap];1.00[ASN][1000 genomes]
rs1245056	1.00[ASN][1000 genomes]
rs1245057	1.00[ASN][1000 genomes]
rs1245058	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1245061	1.00[ASN][1000 genomes]
rs1245063	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs1245067	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs1245068	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs1245069	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs1245072	0.86[ASW][hapmap];0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.80[TSI][hapmap];0.85[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs1261871	1.00[ASN][1000 genomes]
rs1264402	0.86[ASN][1000 genomes]
rs1264403	0.80[ASN][1000 genomes]
rs1264404	0.80[ASN][1000 genomes]
rs1264405	0.80[ASN][1000 genomes]
rs1264407	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs1264408	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs1264409	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs1264410	0.80[ASN][1000 genomes]
rs1264411	0.80[ASN][1000 genomes]
rs1270432	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1270434	1.00[ASN][1000 genomes]
rs1270435	1.00[ASN][1000 genomes]
rs1271928	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.80[TSI][hapmap];1.00[ASN][1000 genomes]
rs1341778	0.86[ASW][hapmap];0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.80[TSI][hapmap]
rs1341779	1.00[ASN][1000 genomes]
rs1341780	1.00[ASN][1000 genomes]
rs1341781	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1361613	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.80[TSI][hapmap];1.00[ASN][1000 genomes]
rs1418007	1.00[ASN][1000 genomes]
rs1418008	1.00[ASN][1000 genomes]
rs1418012	1.00[ASN][1000 genomes]
rs1615332	1.00[ASN][1000 genomes]
rs1618786	0.95[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs1619463	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1622158	1.00[ASN][1000 genomes]
rs1622893	1.00[ASN][1000 genomes]
rs1623673	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.80[TSI][hapmap];1.00[ASN][1000 genomes]
rs1625490	1.00[ASN][1000 genomes]
rs1627769	1.00[ASN][1000 genomes]
rs1628716	1.00[ASN][1000 genomes]
rs1631834	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.80[TSI][hapmap];1.00[ASN][1000 genomes]
rs17324599	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17396516	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1749459	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.80[TSI][hapmap];1.00[ASN][1000 genomes]
rs1749473	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1749484	1.00[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.80[TSI][hapmap]
rs1749485	0.80[ASN][1000 genomes]
rs1749492	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1749494	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1749496	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1749497	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1749498	1.00[ASN][1000 genomes]
rs1749499	0.86[ASW][hapmap];0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.80[TSI][hapmap];1.00[ASN][1000 genomes]
rs1749500	1.00[ASN][1000 genomes]
rs1749502	1.00[ASN][1000 genomes]
rs1749504	1.00[JPT][hapmap]
rs1749506	1.00[ASN][1000 genomes]
rs1749507	0.82[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1749508	1.00[ASN][1000 genomes]
rs1749510	0.87[ASN][1000 genomes]
rs1749512	1.00[ASN][1000 genomes]
rs1749514	1.00[ASN][1000 genomes]
rs1749515	1.00[JPT][hapmap]
rs1749517	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.80[TSI][hapmap];1.00[ASN][1000 genomes]
rs1749520	1.00[ASN][1000 genomes]
rs1773309	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1773313	0.87[ASN][1000 genomes]
rs1773314	1.00[ASN][1000 genomes]
rs1773315	1.00[ASN][1000 genomes]
rs1773316	1.00[ASN][1000 genomes]
rs1773317	1.00[ASN][1000 genomes]
rs1773318	1.00[ASN][1000 genomes]
rs1773319	0.87[ASN][1000 genomes]
rs1773320	1.00[ASN][1000 genomes]
rs1773321	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.80[TSI][hapmap];1.00[ASN][1000 genomes]
rs1773322	1.00[ASN][1000 genomes]
rs1773324	1.00[ASN][1000 genomes]
rs1773325	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.80[TSI][hapmap];1.00[ASN][1000 genomes]
rs1773327	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1773329	1.00[ASN][1000 genomes]
rs1773330	1.00[ASN][1000 genomes]
rs1773332	0.86[ASW][hapmap];0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.80[TSI][hapmap];1.00[ASN][1000 genomes]
rs1773333	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1773335	0.86[ASW][hapmap];0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.80[TSI][hapmap]
rs1773336	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1773337	0.86[ASW][hapmap];0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.80[TSI][hapmap];1.00[ASN][1000 genomes]
rs1773338	1.00[ASN][1000 genomes]
rs1773339	0.84[CEU][hapmap];1.00[JPT][hapmap]
rs1773340	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1773344	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1773346	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1773348	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1773350	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2094037	0.87[ASN][1000 genomes]
rs2094038	1.00[ASN][1000 genomes]
rs2147785	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2209456	1.00[ASN][1000 genomes]
rs227102	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs227104	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs227105	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs227108	0.84[CEU][hapmap];1.00[JPT][hapmap]
rs227114	0.83[CEU][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap]
rs2487762	1.00[ASN][1000 genomes]
rs2487763	1.00[ASN][1000 genomes]
rs2487764	1.00[ASN][1000 genomes]
rs2764522	1.00[ASN][1000 genomes]
rs2764530	0.86[ASW][hapmap];0.89[CEU][hapmap];1.00[JPT][hapmap];0.80[TSI][hapmap]
rs2764532	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2764534	1.00[ASN][1000 genomes]
rs2764535	1.00[ASN][1000 genomes]
rs723993	0.80[ASN][1000 genomes]
rs966069	1.00[ASN][1000 genomes]
rs966070	1.00[ASN][1000 genomes]
rs966071	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	nsv949691	chr1:69749722-70302201	Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	esv3384194	chr1:69885024-70275430	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv830126	chr1:70014879-70167979	Weak transcription Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:70031800-70034200	Active TSS	Fetal Brain Female	brain
2	chr1:70032000-70034000	Active TSS	Brain Hippocampus Middle	brain
3	chr1:70032000-70036400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
4	chr1:70032200-70036800	Active TSS	Brain Inferior Temporal Lobe	brain
5	chr1:70032200-70038400	Active TSS	Brain Anterior Caudate	brain
6	chr1:70032400-70034800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
7	chr1:70032400-70035000	Active TSS	Psoas Muscle	Psoas
8	chr1:70032400-70035200	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
9	chr1:70032400-70035600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr1:70032400-70035600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr1:70032400-70036400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
12	chr1:70032400-70036400	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
13	chr1:70032400-70036400	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
14	chr1:70032400-70036400	Active TSS	Brain Cingulate Gyrus	brain
15	chr1:70032400-70036600	Active TSS	Brain Angular Gyrus	brain
16	chr1:70032400-70036600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
17	chr1:70032600-70034000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr1:70032600-70034000	Bivalent/Poised TSS	NH-A	brain
19	chr1:70032600-70034000	Bivalent/Poised TSS	NHDF-Ad	bronchial
20	chr1:70032600-70034200	Flanking Active TSS	HUVEC	blood vessel
21	chr1:70032600-70034400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr1:70032600-70034400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
23	chr1:70032600-70034400	Bivalent/Poised TSS	Fetal Muscle Leg	muscle
24	chr1:70032600-70034600	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
25	chr1:70032600-70034600	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr1:70032600-70034600	Active TSS	Fetal Kidney	kidney
27	chr1:70032600-70034600	Active TSS	K562	blood
28	chr1:70032600-70035000	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr1:70032600-70035200	Bivalent/Poised TSS	Primary T cells from cord blood	blood
30	chr1:70032600-70035200	Bivalent/Poised TSS	Duodenum Mucosa	Duodenum
31	chr1:70032600-70035400	Active TSS	Pancreatic Islets	Pancreatic Islet
32	chr1:70032600-70035600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
33	chr1:70032600-70035600	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
34	chr1:70032600-70035600	Active TSS	Pancreas	Pancrea
35	chr1:70032600-70035800	Active TSS	Brain Substantia Nigra	brain
36	chr1:70032600-70036000	Bivalent/Poised TSS	Fetal Intestine Large	intestine
37	chr1:70032600-70036200	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
38	chr1:70032600-70036200	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
39	chr1:70032600-70036200	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr1:70032600-70036200	Active TSS	Right Atrium	heart
41	chr1:70032800-70034000	Bivalent/Poised TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr1:70032800-70034000	Active TSS	Gastric	stomach
43	chr1:70032800-70034200	Active TSS	Aorta	Aorta
44	chr1:70032800-70034200	Flanking Active TSS	Liver	Liver
45	chr1:70032800-70034200	Bivalent/Poised TSS	A549	lung
46	chr1:70032800-70034200	Bivalent/Poised TSS	HSMMtube	muscle
47	chr1:70032800-70034400	Flanking Active TSS	Primary hematopoietic stem cells	blood
48	chr1:70032800-70034600	Bivalent/Poised TSS	Thymus	Thymus
49	chr1:70032800-70035000	Bivalent/Poised TSS	NHLF	lung
50	chr1:70032800-70035400	Bivalent/Poised TSS	Primary T helper naive cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links