Variant report

Variant	rs2072939
Chromosome Location	chr1:209801058-209801059
allele	C/T
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	CTCFL	chr1:209801050-209801233	K562	blood:	n/a	n/a
2	MAX	chr1:209800961-209801302	K562	blood:	n/a	n/a
3	CTCF	chr1:209800991-209801551	GM12892	blood:	n/a	chr1:209801175-209801183 chr1:209801163-209801184 chr1:209801168-209801186 chr1:209801170-209801183
4	JUND	chr1:209800961-209801250	H1-hESC	embryonic stem cell:	n/a	chr1:209801135-209801145 chr1:209801055-209801066 chr1:209801053-209801063 chr1:209801134-209801145 chr1:209801135-209801145 chr1:209801134-209801146 chr1:209801054-209801062 chr1:209801135-209801145 chr1:209801135-209801145 chr1:209801052-209801064
5	CTCF	chr1:209801009-209801260	A549	lung:	n/a	chr1:209801175-209801183 chr1:209801163-209801184 chr1:209801168-209801186 chr1:209801170-209801183
6	RAD21	chr1:209800937-209801400	ECC-1	luminal epithelium:	n/a	chr1:209801168-209801180 chr1:209801170-209801180 chr1:209801169-209801182 chr1:209801173-209801187 chr1:209801166-209801185 chr1:209801172-209801186
7	CTCF	chr1:209800823-209801560	GM19238	blood:	n/a	chr1:209801175-209801183 chr1:209801163-209801184 chr1:209801168-209801186 chr1:209801170-209801183
8	MAFK	chr1:209800968-209801306	K562	blood:	n/a	n/a
9	SP4	chr1:209800980-209801337	H1-hESC	embryonic stem cell:	n/a	n/a
10	RAD21	chr1:209800961-209801277	K562	blood:	n/a	chr1:209801168-209801180 chr1:209801170-209801180 chr1:209801169-209801182 chr1:209801173-209801187 chr1:209801166-209801185 chr1:209801172-209801186
11	CTCF	chr1:209801034-209801344	GM10266	blood:	n/a	chr1:209801175-209801183 chr1:209801163-209801184 chr1:209801168-209801186 chr1:209801170-209801183
12	POU2F2	chr1:209800938-209801400	GM12878	blood:	n/a	n/a
13	CTCF	chr1:209801022-209801336	A549	lung:	n/a	chr1:209801175-209801183 chr1:209801163-209801184 chr1:209801168-209801186 chr1:209801170-209801183
14	ATF2	chr1:209800923-209801318	H1-hESC	embryonic stem cell:	n/a	n/a
15	CTCF	chr1:209801016-209801328	H1-hESC	embryonic stem cell:	n/a	chr1:209801175-209801183 chr1:209801163-209801184 chr1:209801168-209801186 chr1:209801170-209801183
16	ZNF143	chr1:209800974-209801342	H1-hESC	embryonic stem cell:	n/a	n/a
17	MAX	chr1:209800847-209801350	NB4	blood:	n/a	n/a
18	SMC3	chr1:209800978-209801384	K562	blood:	n/a	chr1:209801325-209801332 chr1:209801170-209801184
19	ATF2	chr1:209801033-209801333	H1-hESC	embryonic stem cell:	n/a	n/a
20	ZBTB7A	chr1:209800975-209801248	K562	blood:	n/a	n/a
21	POLR2A	chr1:209800943-209801222	Hela-S3	cervix:	n/a	n/a
22	ZC3H11A	chr1:209800965-209801210	K562	blood:	n/a	n/a
23	RAD21	chr1:209800949-209801419	IMR90	lung:	n/a	chr1:209801168-209801180 chr1:209801170-209801180 chr1:209801169-209801182 chr1:209801173-209801187 chr1:209801166-209801185 chr1:209801172-209801186
24	USF2	chr1:209800964-209801384	GM12878	blood:	n/a	n/a
25	MAFK	chr1:209801004-209801315	HepG2	liver:	n/a	n/a
26	CTCF	chr1:209800979-209801335	T-47D	breast:	n/a	chr1:209801175-209801183 chr1:209801163-209801184 chr1:209801168-209801186 chr1:209801170-209801183
27	MAZ	chr1:209800781-209801434	IMR90	lung:	n/a	n/a
28	RAD21	chr1:209800892-209801312	MCF-7	breast:	n/a	chr1:209801168-209801180 chr1:209801170-209801180 chr1:209801169-209801182 chr1:209801173-209801187 chr1:209801166-209801185 chr1:209801172-209801186
29	TCF12	chr1:209800958-209801316	H1-hESC	embryonic stem cell:	n/a	n/a
30	BATF	chr1:209801050-209801312	GM12878	blood:	n/a	chr1:209801137-209801147 chr1:209801136-209801147
31	CTCF	chr1:209801000-209801541	GM19240	blood:	n/a	chr1:209801175-209801183 chr1:209801163-209801184 chr1:209801168-209801186 chr1:209801170-209801183
32	RAD21	chr1:209800694-209801520	HCT-116	colon:	n/a	chr1:209801168-209801180 chr1:209801170-209801180 chr1:209801169-209801182 chr1:209801173-209801187 chr1:209801166-209801185 chr1:209801172-209801186
33	RAD21	chr1:209800943-209801373	SK-N-SH_RA	brain:	n/a	chr1:209801168-209801180 chr1:209801170-209801180 chr1:209801169-209801182 chr1:209801173-209801187 chr1:209801166-209801185 chr1:209801172-209801186
34	RAD21	chr1:209800796-209801467	A549	lung:	n/a	chr1:209801168-209801180 chr1:209801170-209801180 chr1:209801169-209801182 chr1:209801173-209801187 chr1:209801166-209801185 chr1:209801172-209801186
35	CTCF	chr1:209800951-209801328	Kidney_OC	kidney:	n/a	chr1:209801175-209801183 chr1:209801163-209801184 chr1:209801168-209801186 chr1:209801170-209801183
36	CTCF	chr1:209801039-209801310	MCF-7	breast:	n/a	chr1:209801175-209801183 chr1:209801163-209801184 chr1:209801168-209801186 chr1:209801170-209801183
37	ZNF143	chr1:209801013-209801273	Hela-S3	cervix:	n/a	n/a
38	SIN3AK20	chr1:209800941-209801323	SK-N-SH	brain:	n/a	n/a
39	FOS	chr1:209801042-209801058	MCF10A-Er-Src	breast:	n/a	n/a
40	CTCF	chr1:209800956-209801397	K562	blood:	n/a	chr1:209801175-209801183 chr1:209801163-209801184 chr1:209801168-209801186 chr1:209801170-209801183
41	MAFK	chr1:209801023-209801300	IMR90	lung:	n/a	n/a
42	JUND	chr1:209800928-209801352	H1-hESC	embryonic stem cell:	n/a	chr1:209801135-209801145 chr1:209801055-209801066 chr1:209801053-209801063 chr1:209801134-209801145 chr1:209801135-209801145 chr1:209801134-209801146 chr1:209801054-209801062 chr1:209801135-209801145 chr1:209801135-209801145 chr1:209801052-209801064
43	RAD21	chr1:209800646-209801574	SK-N-SH	brain:	n/a	chr1:209801168-209801180 chr1:209801170-209801180 chr1:209801169-209801182 chr1:209801173-209801187 chr1:209801166-209801185 chr1:209801172-209801186
44	ZNF143	chr1:209800963-209801369	GM12878	blood:	n/a	n/a
45	YY1	chr1:209800961-209801356	GM12892	blood:	n/a	n/a
46	JUN	chr1:209801026-209801256	H1-hESC	embryonic stem cell:	n/a	chr1:209801135-209801145 chr1:209801055-209801066 chr1:209801053-209801063 chr1:209801135-209801145 chr1:209801134-209801146 chr1:209801054-209801062 chr1:209801135-209801145 chr1:209801135-209801145 chr1:209801052-209801064
47	FOS	chr1:209800900-209801274	HUVEC	blood vessel:	n/a	chr1:209801135-209801145 chr1:209801134-209801145 chr1:209801055-209801066 chr1:209801053-209801063 chr1:209801135-209801145 chr1:209801134-209801146 chr1:209801052-209801063 chr1:209801054-209801062 chr1:209801135-209801145 chr1:209801135-209801145 chr1:209801052-209801064
48	SMC3	chr1:209800445-209801678	SK-N-SH	brain:	n/a	chr1:209801325-209801332 chr1:209801170-209801184
49	CTCF	chr1:209801035-209801339	A549	lung:	n/a	chr1:209801175-209801183 chr1:209801163-209801184 chr1:209801168-209801186 chr1:209801170-209801183
50	FOSL2	chr1:209800758-209801396	SK-N-SH	brain:	n/a	chr1:209801135-209801145 chr1:209801055-209801066 chr1:209801053-209801063 chr1:209801135-209801145 chr1:209801134-209801146 chr1:209801054-209801062 chr1:209801135-209801145 chr1:209801135-209801145 chr1:209801052-209801064

No.	Distal block	Cell Line	Cell type
1	chr1:209800748..209801330-chr14:23249783..23250303,2	K562	blood:
2	chr1:209742477..209743064-chr1:209800705..209801620,3	K562	blood:
3	chr1:209800921..209801627-chr1:209920949..209921660,2	MCF-7	breast:
4	chr1:209800719..209801238-chr1:209865993..209866698,2	K562	blood:
5	chr1:209800870..209803812-chr1:209809987..209812657,3	K562	blood:
6	chr1:209799563..209802450-chr1:209813916..209816529,2	K562	blood:
7	chr1:209796724..209798782-chr1:209799341..209801502,3	MCF-7	breast:
8	chr1:209749797..209750760-chr1:209800777..209801581,3	MCF-7	breast:
9	chr1:209800950..209802731-chr1:209813916..209816295,2	K562	blood:
10	chr1:209742599..209743311-chr1:209800709..209801256,2	MCF-7	breast:
11	chr1:209775127..209775828-chr1:209800265..209801353,3	MCF-7	breast:
12	chr1:209774955..209775696-chr1:209800756..209801259,2	MCF-7	breast:
13	chr1:209749916..209750746-chr1:209800716..209801439,3	K562	blood:

Variant related genes	Relation type
MIR4260	TF binding region
ENSG00000264831	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10489340	1.00[CEU][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12073223	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12089972	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12090288	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12403733	1.00[CEU][hapmap];0.89[GIH][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12410975	1.00[CEU][hapmap];0.84[GIH][hapmap]
rs17014889	1.00[CEU][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17014906	1.00[CEU][hapmap];0.95[GIH][hapmap];0.82[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17014942	1.00[CEU][hapmap];0.95[GIH][hapmap];0.82[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17014955	1.00[CEU][hapmap];0.80[JPT][hapmap];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17015006	0.82[MEX][hapmap]
rs2072937	1.00[CEU][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2072942	0.91[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2076219	1.00[CEU][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2076222	1.00[CEU][hapmap];0.90[GIH][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2076232	1.00[CEU][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2076347	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2076348	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2076349	1.00[CEU][hapmap];0.95[GIH][hapmap];0.82[EUR][1000 genomes]
rs2076350	0.82[EUR][1000 genomes]
rs2076352	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2229465	1.00[CEU][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2229466	1.00[CEU][hapmap];0.82[GIH][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2235542	1.00[CEU][hapmap];0.95[GIH][hapmap];0.82[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2236889	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2236890	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2282734	0.91[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2282736	0.91[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2282737	0.91[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs36051870	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs58679997	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59815577	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60927005	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs714971	0.96[AMR][1000 genomes];1.00[EUR][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	nsv999901	chr1:209600631-210205379	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	nsv1014034	chr1:209759648-210501731	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:209787200-209808400	Strong transcription	Placenta Amnion	Placenta Amnion
2	chr1:209787400-209816200	Strong transcription	NHEK	skin
3	chr1:209789000-209802800	Strong transcription	Hela-S3	cervix
4	chr1:209791800-209801400	Enhancers	Fetal Muscle Leg	muscle
5	chr1:209792400-209806400	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
6	chr1:209793000-209801600	Enhancers	Ovary	ovary
7	chr1:209793600-209801600	Enhancers	Spleen	Spleen
8	chr1:209794800-209803200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr1:209795200-209804400	Strong transcription	Sigmoid Colon	Sigmoid Colon
10	chr1:209797000-209801400	Enhancers	Fetal Heart	heart
11	chr1:209797000-209801600	Enhancers	Right Ventricle	heart
12	chr1:209797800-209801600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
13	chr1:209797800-209803200	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr1:209798000-209801400	Enhancers	HSMMtube	muscle
15	chr1:209798000-209805200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr1:209798200-209801600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
17	chr1:209798400-209801400	Enhancers	Muscle Satellite Cultured Cells	--
18	chr1:209798400-209801600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr1:209798400-209801600	Enhancers	Left Ventricle	heart
20	chr1:209798600-209801600	Enhancers	Stomach Smooth Muscle	stomach
21	chr1:209798800-209801200	Enhancers	Duodenum Smooth Muscle	Duodenum
22	chr1:209798800-209801200	Enhancers	Fetal Brain Female	brain
23	chr1:209798800-209801600	Enhancers	Brain Cingulate Gyrus	brain
24	chr1:209798800-209801600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
25	chr1:209798800-209801600	Strong transcription	Gastric	stomach
26	chr1:209799000-209801400	Enhancers	Fetal Brain Male	brain
27	chr1:209799000-209801600	Enhancers	Brain Hippocampus Middle	brain
28	chr1:209799000-209801800	Enhancers	Brain Inferior Temporal Lobe	brain
29	chr1:209799200-209801400	Enhancers	Brain Germinal Matrix	brain
30	chr1:209799200-209801400	Genic enhancers	HMEC	breast
31	chr1:209799200-209801600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
32	chr1:209799400-209801200	Enhancers	HSMM	muscle
33	chr1:209799400-209801400	Enhancers	Primary monocytes fromperipheralblood	blood
34	chr1:209799400-209801600	Enhancers	Brain Anterior Caudate	brain
35	chr1:209799400-209806600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr1:209799600-209801600	Enhancers	Primary neutrophils fromperipheralblood	blood
37	chr1:209799600-209801600	Enhancers	Brain Angular Gyrus	brain
38	chr1:209799600-209803600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr1:209799800-209801200	Enhancers	Monocytes-CD14+_RO01746	blood
40	chr1:209799800-209802000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr1:209799800-209814600	Strong transcription	Fetal Intestine Small	intestine
42	chr1:209800000-209801600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr1:209800000-209801600	Bivalent Enhancer	Placenta	Placenta
44	chr1:209800000-209801600	Enhancers	Lung	lung
45	chr1:209800000-209813200	Strong transcription	Fetal Intestine Large	intestine
46	chr1:209800200-209801200	Weak transcription	Fetal Lung	lung
47	chr1:209800200-209801600	Genic enhancers	Colonic Mucosa	Colon
48	chr1:209800200-209801600	Enhancers	Psoas Muscle	Psoas
49	chr1:209800400-209801200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr1:209800400-209801200	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links