Variant report

Variant	rs28446321
Chromosome Location	chr9:98266855-98266856
allele	A/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	JUND	chr9:98266316-98267086	K562	blood:	n/a	chr9:98266473-98266480 chr9:98266470-98266481 chr9:98266471-98266480 chr9:98266936-98266945 chr9:98266656-98266665 chr9:98266475-98266487 chr9:98266470-98266481 chr9:98266471-98266481 chr9:98266468-98266479
2	CTCF	chr9:98266840-98266990	GM12869	blood:	n/a	chr9:98266971-98266980 chr9:98266967-98266980
3	ARID3A	chr9:98266249-98267286	HepG2	liver:	n/a	n/a
4	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
5	CTCF	chr9:98266771-98267105	K562	blood:	n/a	chr9:98266971-98266980 chr9:98266967-98266980
6	CTCF	chr9:98266780-98266930	AoAF	blood vessel:	n/a	n/a
7	ZNF143	chr9:98266683-98267185	H1-hESC	embryonic stem cell:	n/a	n/a
8	MAZ	chr9:98266763-98267180	K562	blood:	n/a	n/a
9	CTCF	chr9:98266836-98267041	K562	blood:	n/a	chr9:98266971-98266980 chr9:98266967-98266980
10	ZNF384	chr9:98266841-98266856	GM12878	blood:	n/a	n/a
11	GATA3	chr9:98266241-98266864	A549	lung:	n/a	n/a
12	CTCF	chr9:98266800-98266950	NHEK	skin:	n/a	n/a
13	RAD21	chr9:98266761-98267144	H1-hESC	embryonic stem cell:	n/a	chr9:98267049-98267058
14	NFYB	chr9:98266749-98267070	K562	blood:	n/a	chr9:98266931-98266943 chr9:98266932-98266947 chr9:98266932-98266946 chr9:98266934-98266944 chr9:98266932-98266945 chr9:98266932-98266947
15	JUN	chr9:98266334-98267165	K562	blood:	n/a	chr9:98266473-98266480 chr9:98266471-98266480 chr9:98266936-98266945 chr9:98266656-98266665 chr9:98266475-98266487 chr9:98266470-98266481 chr9:98266471-98266481 chr9:98266468-98266479
16	MAX	chr9:98266792-98266992	H1-hESC	embryonic stem cell:	n/a	n/a
17	CTCF	chr9:98266820-98266970	GM12871	blood:	n/a	n/a
18	FOXA2	chr9:98266328-98266971	HepG2	liver:	n/a	n/a
19	CTCF	chr9:98266854-98267020	H1-hESC	embryonic stem cell:	n/a	chr9:98266971-98266980 chr9:98266967-98266980
20	CTCF	chr9:98266779-98267100	K562	blood:	n/a	chr9:98266971-98266980 chr9:98266967-98266980
21	SIN3AK20	chr9:98266731-98267174	H1-hESC	embryonic stem cell:	n/a	n/a
22	CTCF	chr9:98266840-98266990	K562	blood:	n/a	chr9:98266971-98266980 chr9:98266967-98266980
23	CTCF	chr9:98266840-98266990	AG10803	skin:	n/a	chr9:98266971-98266980 chr9:98266967-98266980
24	CTCF	chr9:98266840-98266990	HVMF	connective:	n/a	chr9:98266971-98266980 chr9:98266967-98266980
25	MXI1	chr9:98266739-98267190	H1-hESC	embryonic stem cell:	n/a	n/a
26	CTCF	chr9:98266780-98266930	GM12875	blood:	n/a	n/a
27	MAX	chr9:98266688-98267182	H1-hESC	embryonic stem cell:	n/a	chr9:98266760-98266768
28	CTCF	chr9:98266780-98267065	K562	blood:	n/a	chr9:98266971-98266980 chr9:98266967-98266980
29	RAD21	chr9:98266781-98267098	H1-hESC	embryonic stem cell:	n/a	chr9:98267049-98267058
30	HDAC2	chr9:98266702-98267064	K562	blood:	n/a	n/a
31	POLR2A	chr9:98266823-98267173	K562	blood:	n/a	n/a
32	CTCF	chr9:98266840-98266990	GM06990	blood:	n/a	chr9:98266971-98266980 chr9:98266967-98266980
33	MAX	chr9:98266353-98267017	A549	lung:	n/a	chr9:98266760-98266768
34	RCOR1	chr9:98266358-98267391	K562	blood:	n/a	n/a
35	CTCF	chr9:98266835-98266986	HepG2	liver:	n/a	chr9:98266971-98266980 chr9:98266967-98266980
36	RCOR1	chr9:98266593-98267243	K562	blood:	n/a	n/a
37	CTCF	chr9:98266780-98266930	HCPEpiC	choroid plexus:	n/a	n/a
38	CTCF	chr9:98266840-98266990	GM12875	blood:	n/a	chr9:98266971-98266980 chr9:98266967-98266980
39	KAP1	chr9:98266395-98266906	HEK293	kidney:	n/a	n/a
40	CTCF	chr9:98266818-98267021	H1-hESC	embryonic stem cell:	n/a	chr9:98266971-98266980 chr9:98266967-98266980
41	TBL1XR1	chr9:98266389-98266881	K562	blood:	n/a	n/a
42	CTCF	chr9:98266840-98266990	HPF	lung:	n/a	chr9:98266971-98266980 chr9:98266967-98266980
43	CTCF	chr9:98266760-98266910	NHLF	lung:	n/a	n/a
44	CHD1	chr9:98266325-98275163	IMR90	lung:	n/a	chr9:98271086-98271096 chr9:98274530-98274540
45	CTCF	chr9:98266820-98266970	GM12864	blood:	n/a	n/a
46	CTCF	chr9:98266840-98266990	HepG2	liver:	n/a	chr9:98266971-98266980 chr9:98266967-98266980
47	MXI1	chr9:98266653-98267020	K562	blood:	n/a	n/a
48	CTCF	chr9:98266820-98266970	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr9:98243853..98250190-chr9:98264163..98273969,14	MCF-7	breast:
2	chr9:98078830..98081414-chr9:98266391..98270806,3	MCF-7	breast:
3	chr9:98246124..98248586-chr9:98264978..98268110,3	K562	blood:
4	chr9:98187685..98192036-chr9:98266677..98274746,12	MCF-7	breast:
5	chr9:98187278..98190652-chr9:98265637..98273315,6	K562	blood:
6	chr9:98210232..98214386-chr9:98264282..98269915,4	K562	blood:
7	chr9:98253772..98257280-chr9:98266534..98270044,4	K562	blood:
8	chr9:98266714..98268433-chr9:98632145..98634773,2	MCF-7	breast:
9	chr9:98262143..98268122-chr9:98269863..98275996,9	MCF-7	breast:
10	chr9:98187644..98190286-chr9:98266151..98268622,2	K562	blood:

Variant related genes	Relation type
ENSG00000271155	TF binding region
PTCH1	TF binding region
ENSG00000237857	Chromatin interaction
ENSG00000271314	Chromatin interaction
ENSG00000158169	Chromatin interaction
ENSG00000185920	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10512247	0.84[ASN][1000 genomes]
rs10512249	0.96[EUR][1000 genomes]
rs16909892	0.83[EUR][1000 genomes]
rs16909898	0.95[EUR][1000 genomes]
rs16909902	0.95[EUR][1000 genomes]
rs16909904	0.95[EUR][1000 genomes]
rs16909922	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16909978	0.80[ASN][1000 genomes]
rs1805155	0.83[EUR][1000 genomes]
rs2036963	0.93[EUR][1000 genomes]
rs2282040	0.95[EUR][1000 genomes]
rs2282041	0.83[EUR][1000 genomes]
rs2282043	0.93[EUR][1000 genomes]
rs28372566	0.83[EUR][1000 genomes]
rs28377268	0.81[EUR][1000 genomes]
rs28418339	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs28427480	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28446116	0.83[EUR][1000 genomes]
rs28448271	0.95[EUR][1000 genomes]
rs28457693	0.82[EUR][1000 genomes]
rs28474857	0.95[EUR][1000 genomes]
rs28493225	0.92[EUR][1000 genomes]
rs28494679	0.83[EUR][1000 genomes]
rs28510415	0.95[EUR][1000 genomes]
rs28520225	0.83[EUR][1000 genomes]
rs28535536	0.83[EUR][1000 genomes]
rs28583690	0.93[EUR][1000 genomes]
rs28673156	0.95[EUR][1000 genomes]
rs28706464	0.84[EUR][1000 genomes]
rs28711421	0.93[EUR][1000 genomes]
rs3780573	0.95[EUR][1000 genomes]
rs3824488	0.95[EUR][1000 genomes]
rs56149656	0.83[EUR][1000 genomes]
rs59015093	0.83[EUR][1000 genomes]
rs59925771	0.91[EUR][1000 genomes]
rs60150206	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60417486	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs867452	0.83[EUR][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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs28446321	PTCH1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:98240200-98267400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr9:98243000-98267800	Weak transcription	Aorta	Aorta
3	chr9:98254000-98267400	Weak transcription	Small Intestine	intestine
4	chr9:98257400-98267000	Enhancers	Brain Hippocampus Middle	brain
5	chr9:98260800-98267000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr9:98262800-98267600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
7	chr9:98263000-98267800	Weak transcription	Placenta	Placenta
8	chr9:98263000-98267800	Weak transcription	Lung	lung
9	chr9:98264000-98267000	Enhancers	Brain Angular Gyrus	brain
10	chr9:98264000-98267600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
11	chr9:98264200-98267200	Enhancers	Pancreas	Pancrea
12	chr9:98264400-98267200	Enhancers	Primary T helper naive cells from peripheral blood	blood
13	chr9:98264600-98268000	Transcr. at gene 5' and 3'	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr9:98264600-98268000	Weak transcription	Gastric	stomach
15	chr9:98264800-98267200	Enhancers	Fetal Kidney	kidney
16	chr9:98264800-98267200	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr9:98265200-98267400	Enhancers	Primary T killer memory cells from peripheral blood	blood
18	chr9:98265200-98267600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr9:98265400-98267200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr9:98265600-98267400	Enhancers	Cortex derived primary cultured neurospheres	brain
21	chr9:98265600-98267800	Weak transcription	Fetal Muscle Trunk	muscle
22	chr9:98265800-98267400	Enhancers	NHLF	lung
23	chr9:98265800-98268600	Weak transcription	Stomach Mucosa	stomach
24	chr9:98265800-98271600	Active TSS	Rectal Mucosa Donor 29	rectum
25	chr9:98266200-98267400	Enhancers	Breast Myoepithelial Primary Cells	Breast
26	chr9:98266400-98267000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr9:98266400-98267000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr9:98266400-98267000	Flanking Active TSS	Fetal Stomach	stomach
29	chr9:98266400-98267000	Enhancers	Right Ventricle	heart
30	chr9:98266400-98267000	Enhancers	Hela-S3	cervix
31	chr9:98266400-98267200	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
32	chr9:98266400-98267200	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
33	chr9:98266400-98267200	Flanking Active TSS	Fetal Brain Male	brain
34	chr9:98266400-98267200	Enhancers	Fetal Intestine Large	intestine
35	chr9:98266400-98267200	Flanking Active TSS	Ovary	ovary
36	chr9:98266400-98267200	Flanking Active TSS	GM12878-XiMat	blood
37	chr9:98266400-98267400	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
38	chr9:98266400-98267400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr9:98266400-98267400	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
40	chr9:98266400-98267400	Enhancers	HSMMtube	muscle
41	chr9:98266400-98267400	Enhancers	NH-A	brain
42	chr9:98266400-98267400	Enhancers	NHDF-Ad	bronchial
43	chr9:98266400-98267600	Flanking Active TSS	H1 Cell Line	embryonic stem cell
44	chr9:98266400-98267600	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
45	chr9:98266400-98267600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr9:98266400-98267600	Enhancers	Liver	Liver
47	chr9:98266400-98267600	Enhancers	Fetal Muscle Leg	muscle
48	chr9:98266400-98267600	Enhancers	HMEC	breast
49	chr9:98266400-98267800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr9:98266400-98267800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links