Variant report

Variant	rs28377268
Chromosome Location	chr9:98225056-98225057
allele	G/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	WRNIP1	chr9:98224513-98225192	GM12878	blood:	n/a	n/a
2	MAZ	chr9:98224469-98225620	K562	blood:	n/a	chr9:98225514-98225524
3	POLR2A	chr9:98224585-98225555	SK-N-MC	brain:	n/a	n/a
4	ATF2	chr9:98224649-98225239	GM12878	blood:	n/a	n/a
5	YY1	chr9:98224828-98225162	GM12891	blood:	n/a	n/a
6	EP300	chr9:98224492-98225365	GM12878	blood:	n/a	chr9:98224875-98224889
7	RAD21	chr9:98224790-98225196	GM12878	blood:	n/a	n/a
8	PML	chr9:98224716-98225281	GM12878	blood:	n/a	n/a
9	SMC3	chr9:98224520-98225217	GM12878	blood:	n/a	n/a
10	BCLAF1	chr9:98224502-98225248	GM12878	blood:	n/a	chr9:98225195-98225204
11	PAX5	chr9:98224744-98225239	GM12878	blood:	n/a	chr9:98225195-98225204 chr9:98224878-98224887
12	NFIC	chr9:98224636-98225261	SK-N-SH	brain:	n/a	n/a
13	MYC	chr9:98224766-98225290	K562	blood:	n/a	n/a
14	MXI1	chr9:98224719-98225271	K562	blood:	n/a	n/a
15	RELA	chr9:98224675-98225506	GM19193	blood:	n/a	n/a
16	POLR2A	chr9:98224641-98225392	K562	blood:	n/a	n/a
17	MAZ	chr9:98224465-98225741	GM12878	blood:	n/a	chr9:98225514-98225524
18	TAF1	chr9:98224864-98225184	PFSK-1	brain:	n/a	n/a
19	TRIM28	chr9:98224922-98225229	K562	blood:	n/a	n/a
20	POLR2A	chr9:98224686-98225399	K562	blood:	n/a	n/a
21	BCL11A	chr9:98224740-98225225	GM12878	blood:	n/a	chr9:98225195-98225204
22	POLR2A	chr9:98224629-98225729	K562	blood:	n/a	n/a
23	GATA2	chr9:98224617-98225399	K562	blood:	n/a	chr9:98225161-98225169 chr9:98225180-98225189 chr9:98225180-98225190 chr9:98225177-98225193 chr9:98225171-98225188 chr9:98225175-98225196
24	RELA	chr9:98224567-98225634	GM18505	blood:	n/a	n/a
25	FOSL1	chr9:98224771-98225247	K562	blood:	n/a	n/a
26	MYC	chr9:98224866-98225205	HUVEC	blood vessel:	n/a	n/a
27	GATA2	chr9:98224619-98225346	SH-SY5Y	brain:	n/a	chr9:98225161-98225169 chr9:98225180-98225189 chr9:98225180-98225190 chr9:98225177-98225193 chr9:98225171-98225188 chr9:98225175-98225196
28	POLR2A	chr9:98224828-98225229	HUVEC	blood vessel:	n/a	n/a
29	POLR2A	chr9:98224260-98226090	GM12878	blood:	n/a	n/a
30	ZNF274	chr9:98224793-98225259	K562	blood:	n/a	n/a
31	GATA3	chr9:98224844-98225226	SH-SY5Y	brain:	n/a	chr9:98225161-98225169 chr9:98225180-98225189 chr9:98225180-98225190 chr9:98225177-98225193 chr9:98225171-98225188 chr9:98225175-98225196
32	EBF1	chr9:98224673-98225183	GM12878	blood:	n/a	n/a
33	HMGN3	chr9:98224922-98225375	K562	blood:	n/a	n/a
34	MAX	chr9:98224539-98225461	K562	blood:	n/a	n/a
35	POU2F2	chr9:98224513-98225258	GM12891	blood:	n/a	chr9:98225047-98225059
36	POLR2A	chr9:98224688-98225487	K562	blood:	n/a	n/a
37	ELF1	chr9:98224760-98225289	GM12878	blood:	n/a	chr9:98224986-98224999
38	SIN3AK20	chr9:98224887-98225249	SK-N-SH	brain:	n/a	n/a
39	PAX5	chr9:98224723-98225299	GM12878	blood:	n/a	chr9:98225195-98225204 chr9:98224878-98224887
40	NR2F2	chr9:98224799-98225362	K562	blood:	n/a	n/a
41	MEF2C	chr9:98224582-98225298	GM12878	blood:	n/a	n/a
42	YY1	chr9:98224772-98225240	GM12878	blood:	n/a	n/a
43	EP300	chr9:98224688-98225380	SK-N-SH_RA	brain:	n/a	chr9:98224875-98224889
44	TBP	chr9:98224685-98225469	GM12878	blood:	n/a	n/a
45	REST	chr9:98224696-98225265	SK-N-SH	brain:	n/a	chr9:98225238-98225251
46	EGR1	chr9:98224746-98225313	K562	blood:	n/a	chr9:98224904-98224917 chr9:98225050-98225063
47	E2F4	chr9:98224791-98225365	K562	blood:	n/a	n/a
48	POLR2A	chr9:98224686-98225814	GM19099	blood:	n/a	n/a
49	TAF1	chr9:98224704-98225263	GM12878	blood:	n/a	n/a
50	NFIC	chr9:98224460-98225240	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr9:98223864..98226761-chr9:98228381..98231062,3	K562	blood:
2	chr9:98223555..98229775-chr9:98269693..98275962,10	K562	blood:
3	chr9:98218910..98222494-chr9:98224731..98227835,5	K562	blood:
4	chr9:98222977..98229750-chr9:98267050..98274823,12	K562	blood:
5	chr12:53297243..53298949-chr9:98222802..98225552,2	MCF-7	breast:
6	chr9:98223412..98227347-chr9:98253313..98257210,3	K562	blood:

Variant related genes	Relation type
PTCH1	TF binding region
ENSG00000170421	Chromatin interaction
ENSG00000271155	Chromatin interaction
ENSG00000271314	Chromatin interaction
ENSG00000185920	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10512249	0.85[EUR][1000 genomes]
rs16909898	0.86[EUR][1000 genomes]
rs16909902	0.86[EUR][1000 genomes]
rs16909904	0.86[EUR][1000 genomes]
rs16909922	0.81[EUR][1000 genomes]
rs2036963	0.85[EUR][1000 genomes]
rs2282040	0.86[EUR][1000 genomes]
rs2282043	0.85[EUR][1000 genomes]
rs28418339	0.85[EUR][1000 genomes]
rs28427480	0.81[EUR][1000 genomes]
rs28446321	0.81[EUR][1000 genomes]
rs28448271	0.86[EUR][1000 genomes]
rs28457693	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28474857	0.86[EUR][1000 genomes]
rs28493225	0.83[EUR][1000 genomes]
rs28510415	0.86[EUR][1000 genomes]
rs28583690	0.85[EUR][1000 genomes]
rs28673156	0.86[EUR][1000 genomes]
rs28711421	0.85[EUR][1000 genomes]
rs3780573	0.86[EUR][1000 genomes]
rs3824488	0.86[EUR][1000 genomes]
rs59925771	0.82[EUR][1000 genomes]
rs60150206	0.80[EUR][1000 genomes]
rs60417486	0.80[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	nsv949520	chr9:98204199-98238358	Weak transcription Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
4	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
5	nsv1053762	chr9:98208542-98232120	Strong transcription Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases
6	nsv1047465	chr9:98217524-98228225	Transcr. at gene 5' and 3' Weak transcription Genic enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs28377268	PTCH1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:98206000-98237600	Weak transcription	Psoas Muscle	Psoas
2	chr9:98206600-98225200	Strong transcription	Pancreas	Pancrea
3	chr9:98214200-98225400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr9:98218800-98227400	Genic enhancers	Fetal Stomach	stomach
5	chr9:98219400-98225400	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr9:98221400-98226400	Genic enhancers	Fetal Intestine Small	intestine
7	chr9:98221800-98232400	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr9:98223200-98226200	Genic enhancers	Fetal Intestine Large	intestine
9	chr9:98223400-98266400	Weak transcription	Hela-S3	cervix
10	chr9:98223600-98227600	Weak transcription	A549	lung
11	chr9:98224000-98225400	Enhancers	Primary hematopoietic stem cells	blood
12	chr9:98224000-98225800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr9:98224000-98226200	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr9:98224000-98226400	Bivalent Enhancer	Primary B cells from peripheral blood	blood
15	chr9:98224000-98228800	Weak transcription	Liver	Liver
16	chr9:98224200-98225200	Flanking Active TSS	Brain Substantia Nigra	brain
17	chr9:98224200-98225200	Enhancers	Fetal Kidney	kidney
18	chr9:98224200-98225400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr9:98224200-98225400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
20	chr9:98224200-98225800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
21	chr9:98224200-98226200	Enhancers	Cortex derived primary cultured neurospheres	brain
22	chr9:98224200-98226200	Enhancers	Fetal Heart	heart
23	chr9:98224200-98227200	Weak transcription	Gastric	stomach
24	chr9:98224200-98227600	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr9:98224200-98228000	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr9:98224200-98228800	Weak transcription	Right Ventricle	heart
27	chr9:98224200-98229000	Weak transcription	Esophagus	oesophagus
28	chr9:98224400-98225200	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
29	chr9:98224400-98225800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
30	chr9:98224400-98225800	Flanking Active TSS	Fetal Thymus	thymus
31	chr9:98224400-98226000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr9:98224400-98226200	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
33	chr9:98224400-98228800	Weak transcription	HepG2	liver
34	chr9:98224600-98225200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr9:98224600-98225200	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
36	chr9:98224600-98225200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
37	chr9:98224600-98225200	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
38	chr9:98224600-98225200	Flanking Active TSS	Adipose Nuclei	Adipose
39	chr9:98224600-98225200	Flanking Active TSS	Brain Germinal Matrix	brain
40	chr9:98224600-98225200	Flanking Active TSS	Fetal Muscle Trunk	muscle
41	chr9:98224600-98225200	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
42	chr9:98224600-98225200	Flanking Active TSS	Stomach Smooth Muscle	stomach
43	chr9:98224600-98225200	Flanking Active TSS	HUVEC	blood vessel
44	chr9:98224600-98225200	Flanking Active TSS	NH-A	brain
45	chr9:98224600-98225200	Flanking Active TSS	NHEK	skin
46	chr9:98224600-98225400	Transcr. at gene 5' and 3'	HUES6 Cell Line	embryonic stem cell
47	chr9:98224600-98225600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr9:98224600-98225600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr9:98224600-98225800	Genic enhancers	HUES48 Cell Line	embryonic stem cell
50	chr9:98224600-98225800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links