Variant report

Variant	rs11978089
Chromosome Location	chr7:98991181-98991182
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:109)
CpG islands
(count:61)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:109 , 50 per page) page: 1 2 3

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	PML	chr7:98991095-98991564	GM12878	blood:	n/a	n/a
2	POLR2A	chr7:98989498-98998154	PANC-1	pancreas:	n/a	n/a
3	MXI1	chr7:98990309-98991280	H1-hESC	embryonic stem cell:	n/a	n/a
4	ATF2	chr7:98990326-98991423	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr7:98990268-98992339	U87	brain:	n/a	n/a
6	POLR2A	chr7:98990024-98992254	ECC-1	luminal epithelium:	n/a	n/a
7	POLR2A	chr7:98989522-98998944	PANC-1	pancreas:	n/a	n/a
8	TBP	chr7:98990302-98991472	H1-hESC	embryonic stem cell:	n/a	n/a
9	POLR2A	chr7:98990324-98991615	HUVEC	blood vessel:	n/a	n/a
10	POLR2A	chr7:98989637-98992283	HUVEC	blood vessel:	n/a	n/a
11	POLR2A	chr7:98986864-98999101	K562	blood:	n/a	n/a
12	CREB1	chr7:98990223-98991264	H1-hESC	embryonic stem cell:	n/a	n/a
13	POLR2A	chr7:98990386-98992202	GM12878	blood:	n/a	n/a
14	POLR2A	chr7:98989660-98992284	HL-60	blood:	n/a	n/a
15	POLR2A	chr7:98989481-98998177	SK-N-SH	brain:	n/a	n/a
16	POLR2A	chr7:98989722-98992248	K562	blood:	n/a	n/a
17	POLR2A	chr7:98989622-98998764	K562	blood:	n/a	n/a
18	POLR2A	chr7:98989797-98992248	GM19099	blood:	n/a	n/a
19	POLR2A	chr7:98988204-98999255	K562	blood:	n/a	n/a
20	POLR2A	chr7:98989700-98999127	A549	lung:	n/a	n/a
21	POLR2A	chr7:98990160-98992281	HUVEC	blood vessel:	n/a	n/a
22	POLR2A	chr7:98989673-98992223	GM12878	blood:	n/a	n/a
23	MTA3	chr7:98991154-98991674	GM12878	blood:	n/a	n/a
24	POLR2A	chr7:98989876-98991336	ProgFib	skin:	n/a	n/a
25	POLR2A	chr7:98989644-98993973	Hela-S3	cervix:	n/a	n/a
26	MAZ	chr7:98990636-98991335	K562	blood:	n/a	chr7:98991205-98991221 chr7:98990744-98990751 chr7:98990832-98990842 chr7:98990716-98990726 chr7:98991230-98991240 chr7:98990746-98990755
27	NFYB	chr7:98991103-98991378	GM12878	blood:	n/a	n/a
28	USF1	chr7:98991004-98991364	SK-N-SH_RA	brain:	n/a	n/a
29	ZNF143	chr7:98990175-98991437	H1-hESC	embryonic stem cell:	n/a	chr7:98991238-98991247
30	SIN3A	chr7:98990123-98991485	H1-hESC	embryonic stem cell:	n/a	chr7:98990521-98990532
31	MAX	chr7:98990254-98991410	H1-hESC	embryonic stem cell:	n/a	chr7:98991205-98991221 chr7:98990276-98990286 chr7:98990744-98990751 chr7:98990832-98990842 chr7:98990716-98990726 chr7:98991230-98991240 chr7:98990525-98990535 chr7:98990746-98990755
32	USF1	chr7:98990493-98991441	SK-N-SH_RA	brain:	n/a	n/a
33	PBX3	chr7:98990337-98992228	SK-N-SH	brain:	n/a	n/a
34	USF1	chr7:98990413-98991457	ECC-1	luminal epithelium:	n/a	n/a
35	POLR2A	chr7:98990241-98992301	SK-N-SH	brain:	n/a	n/a
36	SIN3AK20	chr7:98990859-98991252	H1-hESC	embryonic stem cell:	n/a	n/a
37	POLR2A	chr7:98991154-98991548	A549	lung:	n/a	n/a
38	POLR2A	chr7:98989619-98992269	K562	blood:	n/a	n/a
39	MXI1	chr7:98989644-98992247	SK-N-SH	brain:	n/a	n/a
40	POLR2A	chr7:98989552-98999005	GM12891	blood:	n/a	n/a
41	PBX3	chr7:98990321-98991521	SK-N-SH	brain:	n/a	n/a
42	POLR2A	chr7:98990227-98991266	H1-neurons	neurons:	n/a	n/a
43	POLR2A	chr7:98989640-98998952	GM12878	blood:	n/a	n/a
44	CHD2	chr7:98990558-98991777	K562	blood:	n/a	n/a
45	TCF12	chr7:98990225-98991263	ECC-1	luminal epithelium:	n/a	n/a
46	SP4	chr7:98990232-98991339	H1-hESC	embryonic stem cell:	n/a	chr7:98990749-98990760 chr7:98990520-98990536 chr7:98990522-98990538 chr7:98991112-98991128 chr7:98990715-98990726 chr7:98990713-98990729 chr7:98991110-98991126 chr7:98990829-98990845
47	CCNT2	chr7:98990150-98991422	K562	blood:	n/a	n/a
48	POLR2A	chr7:98991124-98992157	Hela-S3	cervix:	n/a	n/a
49	POLR2A	chr7:98987820-98994059	HepG2	liver:	n/a	n/a
50	POLR2A	chr7:98989640-98994090	U87	brain:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr7:98991138-98991188	HRE	kidney:	n/a
2	chr7:98991138-98991188	HNPCEpiC	eye:	n/a
3	chr7:98991138-98991188	HCPEpiC	choroid plexus:	n/a
4	chr7:98991138-98991188	NB4	blood:	n/a
5	chr7:98991138-98991188	HepG2	liver:	n/a
6	chr7:98991138-98991188	GM19239	blood:	n/a
7	chr7:98991138-98991188	HMEC	breast:	n/a
8	chr7:98991138-98991188	PFSK-1	brain:	n/a
9	chr7:98991138-98991188	AG10803	skin:	n/a
10	chr7:98991138-98991188	NHDF-neo	bronchial:	n/a
11	chr7:98991138-98991188	SAEC	small airway:	n/a
12	chr7:98991138-98991188	NT2-D1	testis:	n/a
13	chr7:98991138-98991188	HUVEC	blood vessel:	n/a
14	chr7:98991138-98991188	U87	brain:	n/a
15	chr7:98991138-98991188	LNCaP	prostate:	n/a
16	chr7:98991138-98991188	BE2_C	brain:	n/a
17	chr7:98991138-98991188	PANC-1	pancreas:	n/a
18	chr7:98991138-98991188	ECC-1	luminal epithelium:	n/a
19	chr7:98991138-98991188	NH-A	brain:	n/a
20	chr7:98991138-98991188	CMK	blood:	n/a
21	chr7:98991138-98991188	HCF	heart:	n/a
22	chr7:98991138-98991188	GM12878	blood:	n/a
23	chr7:98991138-98991188	IMR90	lung:	fetal
24	chr7:98991138-98991188	SK-N-SH	brain:	n/a
25	chr7:98991138-98991188	GM12892	blood:	n/a
26	chr7:98991138-98991188	AoSMC	blood vessel:	n/a
27	chr7:98991138-98991188	HL-60	blood:	n/a
28	chr7:98991138-98991188	SK-N-SH_RA	brain:	n/a
29	chr7:98991138-98991188	AG04449	skin:	fetal
30	chr7:98991138-98991188	BJ	skin:	n/a
31	chr7:98991138-98991188	Jurkat	blood:	n/a
32	chr7:98991138-98991188	HCT-116	colon:	n/a
33	chr7:98991138-98991188	AG09309	skin:	n/a
34	chr7:98991138-98991188	MCF-7	breast:	n/a
35	chr7:98991138-98991188	PrEC	prostate:	n/a
36	chr7:98991138-98991188	ovcar-3	ovarian:	n/a
37	chr7:98991138-98991188	HRPEpiC	eye:	n/a
38	chr7:98991138-98991188	SK-N-MC	brain:	n/a
39	chr7:98991138-98991188	HEEpiC	esophagus:	n/a
40	chr7:98991138-98991188	GM06990	blood:	n/a
41	chr7:98991138-98991188	HIPEpiC	eye:	n/a
42	chr7:98991138-98991188	A549	lung:	n/a
43	chr7:98991138-98991188	H1-hESC	embryonic stem cell:	embryo
44	chr7:98991138-98991188	Caco-2	colon:	n/a
45	chr7:98991138-98991188	T-47D	breast:	n/a
46	chr7:98991138-98991188	GM12891	blood:	n/a
47	chr7:98991138-98991188	HRCEpiC	kidney:	n/a
48	chr7:98991138-98991188	HPAEpiC	pulmonary alveolar:	n/a
49	chr7:98991138-98991188	HAEpiC	amniotic membrane:	n/a
50	chr7:98991138-98991188	ProgFib	skin:	n/a

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:98988826..98993566-chr7:99002963..99006762,7	MCF-7	breast:
2	chr7:98923537..98926194-chr7:98989828..98992452,2	K562	blood:
3	chr7:98859553..98861919-chr7:98990748..98992511,2	K562	blood:
4	chr7:98970980..98974747-chr7:98986775..98992580,7	MCF-7	breast:
5	chr7:98976910..98979073-chr7:98989172..98991412,2	MCF-7	breast:
6	chr7:98971244..98973231-chr7:98989224..98993180,5	MCF-7	breast:
7	chr7:98966757..98974253-chr7:98988800..98995304,7	K562	blood:

No data

Variant related genes	Relation type
ARPC1B	TF binding region
ARPC1B	CpG island
ENSG00000106245	Chromatin interaction
ENSG00000106244	Chromatin interaction
ENSG00000241685	Chromatin interaction
ENSG00000130429	Chromatin interaction
ENSG00000002079	Chromatin interaction

Extended variants
information (count: 99 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:96)

rs_ID	r²[population]
rs10155966	0.91[CEU][hapmap];0.84[EUR][1000 genomes]
rs10225529	0.97[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10238965	0.84[CEU][hapmap]
rs10243678	0.91[CEU][hapmap];0.87[EUR][1000 genomes]
rs10249167	0.82[EUR][1000 genomes]
rs10251282	0.95[ASN][1000 genomes]
rs10255399	0.81[EUR][1000 genomes]
rs10258757	0.91[CEU][hapmap];0.81[EUR][1000 genomes]
rs10270459	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs10270917	0.91[CEU][hapmap];0.81[EUR][1000 genomes]
rs10271049	0.84[CEU][hapmap]
rs10272998	0.91[CEU][hapmap]
rs10277149	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10279308	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1043466	0.84[CEU][hapmap]
rs1045012	1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs11762273	0.91[CEU][hapmap];0.83[EUR][1000 genomes]
rs11771702	0.91[CEU][hapmap]
rs11976018	0.84[CEU][hapmap]
rs12112936	0.91[CEU][hapmap]
rs12113440	0.91[CEU][hapmap]
rs12538893	0.83[CEU][hapmap]
rs17161662	0.81[CEU][hapmap]
rs17161669	0.81[CEU][hapmap]
rs17161695	0.91[CEU][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17161700	1.00[JPT][hapmap]
rs17161726	1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs17854665	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs1980307	0.84[CEU][hapmap]
rs2003499	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2072181	0.91[CEU][hapmap];0.85[EUR][1000 genomes]
rs2240384	0.84[CEU][hapmap]
rs2272168	0.85[CEU][hapmap]
rs2280600	0.84[CEU][hapmap]
rs2280601	0.84[CEU][hapmap]
rs2286162	0.92[CEU][hapmap]
rs2293256	1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2404323	0.82[EUR][1000 genomes]
rs2404487	0.95[ASN][1000 genomes]
rs2404488	0.95[ASN][1000 genomes]
rs28377312	1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs28460612	0.95[ASN][1000 genomes]
rs28495024	0.85[EUR][1000 genomes]
rs28558950	1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs28668326	1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs28753399	0.95[ASN][1000 genomes]
rs3137	0.85[CEU][hapmap]
rs34943973	0.95[ASN][1000 genomes]
rs3528	0.95[ASN][1000 genomes]
rs3801288	0.91[CEU][hapmap]
rs3823813	0.89[ASN][1000 genomes]
rs41385645	1.00[JPT][hapmap]
rs45441991	0.89[ASN][1000 genomes]
rs45448997	0.95[ASN][1000 genomes]
rs45451992	0.95[ASN][1000 genomes]
rs45461000	0.95[ASN][1000 genomes]
rs45492501	0.89[ASN][1000 genomes]
rs45529541	0.89[ASN][1000 genomes]
rs45555335	0.89[ASN][1000 genomes]
rs45592335	0.89[ASN][1000 genomes]
rs4729532	1.00[CEU][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs55927283	0.89[ASN][1000 genomes]
rs55942267	0.95[ASN][1000 genomes]
rs56167514	0.89[ASN][1000 genomes]
rs57367781	0.89[ASN][1000 genomes]
rs59240302	0.89[ASN][1000 genomes]
rs59672032	0.95[ASN][1000 genomes]
rs6943920	0.92[CEU][hapmap];0.84[EUR][1000 genomes]
rs6955490	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6957987	0.82[CEU][hapmap]
rs6962772	0.84[CEU][hapmap]
rs6974831	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs73397447	0.95[ASN][1000 genomes]
rs73397481	0.95[ASN][1000 genomes]
rs73397499	0.95[ASN][1000 genomes]
rs733991	0.91[CEU][hapmap]
rs73401507	0.95[ASN][1000 genomes]
rs73401510	0.95[ASN][1000 genomes]
rs73401516	0.95[ASN][1000 genomes]
rs73403247	0.89[ASN][1000 genomes]
rs73403272	0.89[ASN][1000 genomes]
rs73403286	0.89[ASN][1000 genomes]
rs73403290	0.89[ASN][1000 genomes]
rs73405247	0.89[ASN][1000 genomes]
rs73711280	0.95[ASN][1000 genomes]
rs73711293	0.89[ASN][1000 genomes]
rs73711294	0.89[ASN][1000 genomes]
rs73713507	0.89[ASN][1000 genomes]
rs73713531	0.84[ASN][1000 genomes]
rs7794068	0.89[ASN][1000 genomes]
rs7794705	0.85[CEU][hapmap]
rs7805661	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs883403	0.85[CEU][hapmap]
rs917152	1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs917154	0.83[CEU][hapmap]
rs952319	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[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	esv3433144	chr7:98777878-99060209	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
2	nsv831068	chr7:98819572-99006481	Weak transcription Active TSS Genic enhancers Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
3	nsv831069	chr7:98948128-99127584	Active TSS Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:98979400-99001800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr7:98980400-99003800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
3	chr7:98980800-99000600	Strong transcription	Dnd41	blood
4	chr7:98981000-98993000	Strong transcription	A549	lung
5	chr7:98985600-99003800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr7:98986200-98992000	Weak transcription	HSMMtube	muscle
7	chr7:98987000-99004200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr7:98989600-98991400	Active TSS	HUES48 Cell Line	embryonic stem cell
9	chr7:98989600-98991400	Active TSS	iPS-18 Cell Line	embryonic stem cell
10	chr7:98989600-98991600	Genic enhancers	HMEC	breast
11	chr7:98989800-98991200	Active TSS	H1 Cell Line	embryonic stem cell
12	chr7:98989800-98991200	Active TSS	H9 Cell Line	embryonic stem cell
13	chr7:98989800-98991200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr7:98989800-98991200	Active TSS	HUES64 Cell Line	embryonic stem cell
15	chr7:98989800-98991200	Active TSS	iPS-15b Cell Line	embryonic stem cell
16	chr7:98989800-98991200	Active TSS	Brain Cingulate Gyrus	brain
17	chr7:98989800-98991200	Weak transcription	HepG2	liver
18	chr7:98989800-98991400	Active TSS	ES-I3 Cell Line	embryonic stem cell
19	chr7:98989800-98991400	Active TSS	iPS-20b Cell Line	embryonic stem cell
20	chr7:98989800-98991600	Genic enhancers	Primary B cells from cord blood	blood
21	chr7:98989800-98991600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
22	chr7:98989800-98991600	Flanking Active TSS	Stomach Smooth Muscle	stomach
23	chr7:98989800-98992000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr7:98990000-98991200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr7:98990000-98991200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
26	chr7:98990000-98991200	Transcr. at gene 5' and 3'	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr7:98990000-98991200	Active TSS	Brain Germinal Matrix	brain
28	chr7:98990000-98991200	Active TSS	Rectal Smooth Muscle	rectum
29	chr7:98990000-98991400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr7:98990000-98991400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr7:98990000-98991400	Transcr. at gene 5' and 3'	Fetal Intestine Small	intestine
32	chr7:98990000-98991400	Flanking Active TSS	Right Ventricle	heart
33	chr7:98990000-98991600	Transcr. at gene 5' and 3'	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr7:98990000-98991600	Flanking Active TSS	Colonic Mucosa	Colon
35	chr7:98990000-98991600	Active TSS	Pancreatic Islets	Pancreatic Islet
36	chr7:98990000-98991600	Genic enhancers	NHLF	lung
37	chr7:98990000-98992000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr7:98990000-99002800	Strong transcription	GM12878-XiMat	blood
39	chr7:98990200-98991200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr7:98990200-98991200	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr7:98990200-98991200	Active TSS	HUES6 Cell Line	embryonic stem cell
42	chr7:98990200-98991200	Active TSS	Breast Myoepithelial Primary Cells	Breast
43	chr7:98990200-98991200	Transcr. at gene 5' and 3'	Primary B cells from peripheral blood	blood
44	chr7:98990200-98991200	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
45	chr7:98990200-98991200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr7:98990200-98991200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr7:98990200-98991200	Transcr. at gene 5' and 3'	Primary mononuclear cells fromperipheralblood	Blood
48	chr7:98990200-98991200	Active TSS	Brain Angular Gyrus	brain
49	chr7:98990200-98991200	Active TSS	Colon Smooth Muscle	Colon
50	chr7:98990200-98991200	Active TSS	Fetal Intestine Large	intestine

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