Variant report

Variant	rs1877456
Chromosome Location	chr9:98275097-98275098
allele	C/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	SIN3A	chr9:98266518-98275316	H1-hESC	embryonic stem cell:	n/a	chr9:98268478-98268491 chr9:98273259-98273270 chr9:98273104-98273113 chr9:98271212-98271225 chr9:98270756-98270767 chr9:98271270-98271279 chr9:98272257-98272268 chr9:98273102-98273111 chr9:98271251-98271264
2	SPI1	chr9:98274896-98275477	HL-60	blood:	n/a	n/a
3	CEBPB	chr9:98275022-98275333	Hela-S3	cervix:	n/a	chr9:98275097-98275109
4	POLR2A	chr9:98274240-98275220	H1-neurons	neurons:	n/a	n/a
5	HEY1	chr9:98272980-98275121	K562	blood:	n/a	n/a
6	RCOR1	chr9:98274919-98275143	K562	blood:	n/a	n/a
7	CEBPB	chr9:98275082-98275317	K562	blood:	n/a	chr9:98275097-98275109
8	MAZ	chr9:98272840-98275341	K562	blood:	n/a	chr9:98273103-98273112 chr9:98273840-98273850 chr9:98273839-98273852 chr9:98273839-98273852 chr9:98273101-98273114 chr9:98273839-98273854 chr9:98273102-98273113 chr9:98274378-98274387 chr9:98273844-98273852 chr9:98273101-98273114 chr9:98273839-98273852 chr9:98273103-98273112
9	MYC	chr9:98272814-98275318	K562	blood:	n/a	chr9:98273103-98273112 chr9:98273840-98273850 chr9:98273839-98273852 chr9:98273839-98273852 chr9:98273101-98273114 chr9:98273839-98273854 chr9:98273102-98273113 chr9:98274378-98274387 chr9:98273844-98273852 chr9:98273101-98273114 chr9:98273839-98273852 chr9:98273103-98273112
10	TAL1	chr9:98275000-98275462	K562	blood:	n/a	n/a
11	SPI1	chr9:98275013-98275323	K562	blood:	n/a	n/a
12	TEAD4	chr9:98274604-98275100	H1-hESC	embryonic stem cell:	n/a	n/a
13	CEBPB	chr9:98274814-98275362	K562	blood:	n/a	chr9:98275097-98275109
14	POLR2A	chr9:98272794-98275319	K562	blood:	n/a	n/a
15	SP1	chr9:98274557-98275158	H1-hESC	embryonic stem cell:	n/a	chr9:98274657-98274666 chr9:98274656-98274670
16	UBTF	chr9:98275036-98275175	K562	blood:	n/a	n/a
17	POLR2A	chr9:98272809-98275351	K562	blood:	n/a	n/a
18	MAX	chr9:98272839-98275152	H1-hESC	embryonic stem cell:	n/a	chr9:98273103-98273112 chr9:98273840-98273850 chr9:98273839-98273852 chr9:98273839-98273852 chr9:98273101-98273114 chr9:98273839-98273854 chr9:98273102-98273113 chr9:98274378-98274387 chr9:98273844-98273852 chr9:98273101-98273114 chr9:98273839-98273852 chr9:98273103-98273112
19	POLR2A	chr9:98272731-98275257	K562	blood:	n/a	n/a
20	CEBPB	chr9:98274926-98275332	K562	blood:	n/a	chr9:98275097-98275109
21	ZMIZ1	chr9:98274211-98275425	K562	blood:	n/a	n/a
22	BHLHE40	chr9:98272876-98275139	K562	blood:	n/a	chr9:98273204-98273220 chr9:98273841-98273850 chr9:98273841-98273850
23	POLR2A	chr9:98272435-98275174	SK-N-MC	brain:	n/a	n/a
24	MYC	chr9:98272581-98275186	K562	blood:	n/a	chr9:98273103-98273112 chr9:98273840-98273850 chr9:98273839-98273852 chr9:98273839-98273852 chr9:98273101-98273114 chr9:98273839-98273854 chr9:98273102-98273113 chr9:98274378-98274387 chr9:98273844-98273852 chr9:98273101-98273114 chr9:98273839-98273852 chr9:98273103-98273112
25	SMC3	chr9:98274719-98275310	K562	blood:	n/a	n/a
26	EP300	chr9:98275093-98275369	K562	blood:	n/a	chr9:98275181-98275195
27	SPI1	chr9:98275002-98275281	K562	blood:	n/a	n/a
28	MYC	chr9:98272592-98275333	K562	blood:	n/a	chr9:98273103-98273112 chr9:98273840-98273850 chr9:98273839-98273852 chr9:98273839-98273852 chr9:98273101-98273114 chr9:98273839-98273854 chr9:98273102-98273113 chr9:98274378-98274387 chr9:98273844-98273852 chr9:98273101-98273114 chr9:98273839-98273852 chr9:98273103-98273112
29	RAD21	chr9:98274726-98275258	H1-hESC	embryonic stem cell:	n/a	n/a
30	POLR2A	chr9:98272783-98275491	K562	blood:	n/a	n/a
31	JUND	chr9:98275017-98275374	K562	blood:	n/a	n/a
32	MYC	chr9:98272920-98275321	NB4	blood:	n/a	chr9:98273103-98273112 chr9:98273840-98273850 chr9:98273839-98273852 chr9:98273839-98273852 chr9:98273101-98273114 chr9:98273839-98273854 chr9:98273102-98273113 chr9:98274378-98274387 chr9:98273844-98273852 chr9:98273101-98273114 chr9:98273839-98273852 chr9:98273103-98273112
33	POLR2A	chr9:98271292-98278496	K562	blood:	n/a	n/a
34	CTCF	chr9:98275020-98275170	HEK293	kidney:	n/a	chr9:98275137-98275155
35	MXI1	chr9:98267369-98275571	SK-N-SH	brain:	n/a	chr9:98273104-98273113 chr9:98269404-98269413
36	TEAD4	chr9:98274678-98275443	K562	blood:	n/a	n/a
37	MAX	chr9:98272781-98275234	K562	blood:	n/a	chr9:98273103-98273112 chr9:98273840-98273850 chr9:98273839-98273852 chr9:98273839-98273852 chr9:98273101-98273114 chr9:98273839-98273854 chr9:98273102-98273113 chr9:98274378-98274387 chr9:98273844-98273852 chr9:98273101-98273114 chr9:98273839-98273852 chr9:98273103-98273112
38	POLR2A	chr9:98274163-98275164	K562	blood:	n/a	n/a
39	TEAD4	chr9:98274651-98275098	H1-hESC	embryonic stem cell:	n/a	n/a
40	POLR2A	chr9:98274860-98275263	K562	blood:	n/a	n/a
41	SP1	chr9:98274691-98275099	H1-hESC	embryonic stem cell:	n/a	n/a
42	POLR2A	chr9:98272547-98275105	Hela-S3	cervix:	n/a	n/a
43	POLR2A	chr9:98274905-98275356	K562	blood:	n/a	n/a
44	MYC	chr9:98274927-98275134	MCF10A-Er-Src	breast:	n/a	n/a
45	ARID3A	chr9:98274275-98275452	K562	blood:	n/a	n/a
46	SPI1	chr9:98274950-98275290	HL-60	blood:	n/a	n/a
47	TBP	chr9:98272687-98275302	K562	blood:	n/a	n/a
48	CHD1	chr9:98266325-98275163	IMR90	lung:	n/a	chr9:98271086-98271096 chr9:98274530-98274540
49	MAX	chr9:98272820-98275299	NB4	blood:	n/a	chr9:98273103-98273112 chr9:98273840-98273850 chr9:98273839-98273852 chr9:98273839-98273852 chr9:98273101-98273114 chr9:98273839-98273854 chr9:98273102-98273113 chr9:98274378-98274387 chr9:98273844-98273852 chr9:98273101-98273114 chr9:98273839-98273852 chr9:98273103-98273112
50	CEBPB	chr9:98274994-98275285	IMR90	lung:	n/a	chr9:98275097-98275109

No.	Distal block	Cell Line	Cell type
1	chr9:98273384..98275933-chr9:98636308..98638563,2	K562	blood:
2	chr9:98255343..98257866-chr9:98273112..98275130,2	K562	blood:
3	chr9:98274022..98276017-chr9:99178559..99180627,2	K562	blood:
4	chr9:98172380..98174560-chr9:98273339..98275804,2	K562	blood:
5	chr9:98073533..98075085-chr9:98273778..98276270,2	K562	blood:
6	chr9:98186276..98191956-chr9:98269234..98276633,9	K562	blood:
7	chr9:98078136..98081236-chr9:98271605..98275803,7	K562	blood:
8	chr9:98143874..98147656-chr9:98271045..98275159,6	MCF-7	breast:
9	chr9:98273168..98275933-chr9:98636308..98638563,3	K562	blood:
10	chr9:98270649..98275167-chr9:98636318..98639773,5	MCF-7	breast:
11	chr9:98010532..98014660-chr9:98272495..98275814,3	K562	blood:
12	chr9:98078212..98082706-chr9:98271985..98275473,10	K562	blood:
13	chr9:98272365..98275151-chr9:98293260..98296891,4	K562	blood:
14	chr9:98262143..98268122-chr9:98269863..98275996,9	MCF-7	breast:

Variant related genes	Relation type
ENSG00000271659	TF binding region
PTCH1	TF binding region
ENSG00000271314	Chromatin interaction
ENSG00000175611	Chromatin interaction
ENSG00000237857	Chromatin interaction
ENSG00000182150	Chromatin interaction
ENSG00000165244	Chromatin interaction
ENSG00000185920	Chromatin interaction
ENSG00000158169	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs17369383	0.81[EUR][1000 genomes]
rs28410513	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28411363	0.81[EUR][1000 genomes]
rs28412122	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28468571	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28485705	0.97[EUR][1000 genomes]
rs28488553	0.81[EUR][1000 genomes]
rs28491365	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28504341	0.81[EUR][1000 genomes]
rs28704635	0.87[EUR][1000 genomes]
rs28705285	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3758301	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531633	chr9:98078300-98431120	Flanking Active TSS Active TSS Strong transcription Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
2	nsv831658	chr9:98152971-98342178	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv430083	chr9:98204245-98445645	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
4	nsv824994	chr9:98239963-98314431	Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv824995	chr9:98243455-98326547	Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv824996	chr9:98245375-98283861	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:98272400-98275200	Active TSS	Colonic Mucosa	Colon
2	chr9:98272800-98276000	Active TSS	Rectal Mucosa Donor 29	rectum
3	chr9:98273600-98275200	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
4	chr9:98273800-98275200	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
5	chr9:98273800-98275200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr9:98273800-98275400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr9:98273800-98275400	Flanking Active TSS	Fetal Intestine Small	intestine
8	chr9:98273800-98275600	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
9	chr9:98273800-98277800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr9:98274000-98275200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr9:98274000-98275200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr9:98274000-98275200	Enhancers	Lung	lung
13	chr9:98274000-98275400	Flanking Active TSS	Hela-S3	cervix
14	chr9:98274000-98277800	Weak transcription	Gastric	stomach
15	chr9:98274200-98275200	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr9:98274200-98275200	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr9:98274200-98275200	Enhancers	Placenta Amnion	Placenta Amnion
18	chr9:98274200-98275400	Enhancers	Spleen	Spleen
19	chr9:98274200-98275400	Flanking Active TSS	NHEK	skin
20	chr9:98274200-98277400	Active TSS	Rectal Smooth Muscle	rectum
21	chr9:98274200-98278000	Weak transcription	Aorta	Aorta
22	chr9:98274400-98275200	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
23	chr9:98274400-98275200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr9:98274400-98275200	Enhancers	Primary T helper cells fromperipheralblood	blood
25	chr9:98274400-98275200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr9:98274400-98275200	Enhancers	Duodenum Smooth Muscle	Duodenum
27	chr9:98274400-98275600	Active TSS	Stomach Smooth Muscle	stomach
28	chr9:98274400-98277200	Active TSS	Rectal Mucosa Donor 31	rectum
29	chr9:98274400-98277600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
30	chr9:98274400-98277600	Weak transcription	Colon Smooth Muscle	Colon
31	chr9:98274400-98278000	Weak transcription	Pancreatic Islets	Pancreatic Islet
32	chr9:98274600-98275200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
33	chr9:98274600-98275200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr9:98274600-98275200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr9:98274600-98275200	Enhancers	Brain Inferior Temporal Lobe	brain
36	chr9:98274600-98275200	Enhancers	Right Atrium	heart
37	chr9:98274600-98275200	Flanking Active TSS	NHLF	lung
38	chr9:98274600-98275400	Enhancers	Brain Cingulate Gyrus	brain
39	chr9:98274600-98275400	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
40	chr9:98274600-98275600	Enhancers	Fetal Heart	heart
41	chr9:98274600-98278000	Weak transcription	Pancreas	Pancrea
42	chr9:98274600-98279600	Active TSS	Duodenum Mucosa	Duodenum
43	chr9:98274800-98275200	Flanking Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr9:98274800-98275200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr9:98274800-98275200	Flanking Bivalent TSS/Enh	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr9:98274800-98275200	Enhancers	Breast Myoepithelial Primary Cells	Breast
47	chr9:98274800-98275200	Bivalent Enhancer	Fetal Muscle Leg	muscle
48	chr9:98274800-98275200	Flanking Active TSS	Fetal Stomach	stomach
49	chr9:98274800-98275200	Enhancers	Ovary	ovary
50	chr9:98274800-98275200	Weak transcription	Right Ventricle	heart

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