Variant report

Variant	rs1800247
Chromosome Location	chr1:156211825-156211826
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:35)
CpG islands
(count:61)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:35 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:156210487-156212938	GM12892	blood:	n/a	n/a
2	POLR2A	chr1:156210700-156213351	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr1:156210499-156212419	GM12892	blood:	n/a	n/a
4	POLR2A	chr1:156211622-156212567	GM12878	blood:	n/a	n/a
5	POLR2A	chr1:156210661-156212093	PANC-1	pancreas:	n/a	n/a
6	ELF1	chr1:156211540-156211917	GM12878	blood:	n/a	n/a
7	POLR2A	chr1:156210560-156211845	H1-hESC	embryonic stem cell:	n/a	n/a
8	POLR2A	chr1:156211679-156212371	Hela-S3	cervix:	n/a	n/a
9	POLR2A	chr1:156210570-156218256	HepG2	liver:	n/a	n/a
10	POLR2A	chr1:156210568-156213182	ECC-1	luminal epithelium:	n/a	n/a
11	POLR2A	chr1:156210453-156214323	K562	blood:	n/a	n/a
12	POLR2A	chr1:156210495-156213068	GM12891	blood:	n/a	n/a
13	RUNX3	chr1:156211646-156211963	GM12878	blood:	n/a	n/a
14	POLR2A	chr1:156210596-156214175	A549	lung:	n/a	n/a
15	EBF1	chr1:156211763-156212043	GM12878	blood:	n/a	n/a
16	POLR2A	chr1:156210858-156212300	SK-N-MC	brain:	n/a	n/a
17	POLR2A	chr1:156211051-156211881	ECC-1	luminal epithelium:	n/a	n/a
18	POLR2A	chr1:156211778-156211872	ProgFib	skin:	n/a	n/a
19	POLR2A	chr1:156210609-156213021	MCF-7	breast:	n/a	n/a
20	POLR2A	chr1:156211808-156212650	K562	blood:	n/a	n/a
21	POLR2A	chr1:156210543-156215767	Hela-S3	cervix:	n/a	n/a
22	POLR2A	chr1:156211668-156213149	Hela-S3	cervix:	n/a	n/a
23	MAZ	chr1:156211260-156211854	IMR90	lung:	n/a	chr1:156211654-156211664
24	POLR2A	chr1:156210688-156212977	K562	blood:	n/a	n/a
25	POLR2A	chr1:156211710-156212322	A549	lung:	n/a	n/a
26	BCL3	chr1:156211194-156211914	A549	lung:	n/a	n/a
27	POLR2A	chr1:156210640-156213065	H1-hESC	embryonic stem cell:	n/a	n/a
28	POLR2A	chr1:156210363-156213159	GM12892	blood:	n/a	n/a
29	POLR2A	chr1:156210581-156218305	Hela-S3	cervix:	n/a	n/a
30	RUNX3	chr1:156211585-156211965	GM12878	blood:	n/a	n/a
31	POLR2A	chr1:156210492-156213047	GM12878	blood:	n/a	n/a
32	POLR2A	chr1:156211783-156212227	H1-neurons	neurons:	n/a	n/a
33	POLR2A	chr1:156210557-156213065	GM12878	blood:	n/a	n/a
34	POLR2A	chr1:156210501-156213072	GM12891	blood:	n/a	n/a
35	POLR2A	chr1:156210424-156212639	GM12891	blood:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr1:156211801-156211851	HCPEpiC	choroid plexus:	n/a
2	chr1:156211801-156211851	HPAEpiC	pulmonary alveolar:	n/a
3	chr1:156211801-156211851	SKMC	muscle:	n/a
4	chr1:156211801-156211851	NHBE	bronchial:	n/a
5	chr1:156211801-156211851	PrEC	prostate:	n/a
6	chr1:156211801-156211851	HCM	heart:	n/a
7	chr1:156211801-156211851	HMEC	breast:	n/a
8	chr1:156211801-156211851	H1-hESC	embryonic stem cell:	embryo
9	chr1:156211801-156211851	Caco-2	colon:	n/a
10	chr1:156211801-156211851	GM19239	blood:	n/a
11	chr1:156211801-156211851	HCT-116	colon:	n/a
12	chr1:156211801-156211851	HEK293	kidney:	embryo
13	chr1:156211801-156211851	U87	brain:	n/a
14	chr1:156211801-156211851	LNCaP	prostate:	n/a
15	chr1:156211801-156211851	HL-60	blood:	n/a
16	chr1:156211801-156211851	PFSK-1	brain:	n/a
17	chr1:156211801-156211851	Jurkat	blood:	n/a
18	chr1:156211801-156211851	GM12892	blood:	n/a
19	chr1:156211801-156211851	HNPCEpiC	eye:	n/a
20	chr1:156211801-156211851	BE2_C	brain:	n/a
21	chr1:156211801-156211851	A549	lung:	n/a
22	chr1:156211801-156211851	HIPEpiC	eye:	n/a
23	chr1:156211801-156211851	Hepatocyte	liver:	n/a
24	chr1:156211801-156211851	HUVEC	blood vessel:	n/a
25	chr1:156211801-156211851	GM12891	blood:	n/a
26	chr1:156211801-156211851	NH-A	brain:	n/a
27	chr1:156211801-156211851	GM12878	blood:	n/a
28	chr1:156211801-156211851	MCF10A-Er-Src	breast:	n/a
29	chr1:156211801-156211851	SK-N-SH_RA	brain:	n/a
30	chr1:156211801-156211851	HEEpiC	esophagus:	n/a
31	chr1:156211801-156211851	K562	blood:	n/a
32	chr1:156211801-156211851	MCF-7	breast:	n/a
33	chr1:156211801-156211851	CMK	blood:	n/a
34	chr1:156211801-156211851	AoSMC	blood vessel:	n/a
35	chr1:156211801-156211851	SK-N-SH	brain:	n/a
36	chr1:156211801-156211851	NB4	blood:	n/a
37	chr1:156211801-156211851	SAEC	small airway:	n/a
38	chr1:156211801-156211851	BJ	skin:	n/a
39	chr1:156211801-156211851	AG09309	skin:	n/a
40	chr1:156211801-156211851	PANC-1	pancreas:	n/a
41	chr1:156211801-156211851	ECC-1	luminal epithelium:	n/a
42	chr1:156211801-156211851	HepG2	liver:	n/a
43	chr1:156211801-156211851	IMR90	lung:	fetal
44	chr1:156211801-156211851	HRE	kidney:	n/a
45	chr1:156211801-156211851	ovcar-3	ovarian:	n/a
46	chr1:156211801-156211851	AG09319	gingival:	n/a
47	chr1:156211801-156211851	HRPEpiC	eye:	n/a
48	chr1:156211801-156211851	T-47D	breast:	n/a
49	chr1:156211801-156211851	AG04449	skin:	fetal
50	chr1:156211801-156211851	HAEpiC	amniotic membrane:	n/a

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:156118455..156120735-chr1:156211207..156213890,2	MCF-7	breast:
2	chr1:156104742..156107610-chr1:156210647..156213475,2	K562	blood:

No data

Variant related genes	Relation type
BGLAP	TF binding region
BGLAP	CpG island
ENSG00000196189	Chromatin interaction
ENSG00000160789	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs2246476	0.90[ASN][1000 genomes]
rs2253358	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2540168	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2540169	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916198	chr1:155804210-156403997	Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	428 gene(s)	inside rSNPs	diseases
2	nsv1011302	chr1:156081561-156532624	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	380 gene(s)	inside rSNPs	diseases
3	nsv872470	chr1:156210557-156223823	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases
4	esv3397794	chr1:156210878-156213676	Strong transcription Genic enhancers Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	n/a
5	nsv547967	chr1:156211476-156217855	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	n/a

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1800247	C1orf85	cis	Whole Blood	GTEx
rs1800247	SMG5	cis	Whole Blood	GTEx
rs1800247	PAQR6	cis	Whole Blood	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:156186800-156214600	Weak transcription	Stomach Mucosa	stomach
2	chr1:156188400-156215200	Weak transcription	Right Atrium	heart
3	chr1:156189200-156213800	Strong transcription	Fetal Stomach	stomach
4	chr1:156192000-156214200	Weak transcription	Fetal Brain Male	brain
5	chr1:156195000-156212600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr1:156196000-156212600	Strong transcription	Placenta	Placenta
7	chr1:156196000-156214200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr1:156201200-156214000	Strong transcription	Fetal Muscle Leg	muscle
9	chr1:156201400-156213600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr1:156201600-156212600	Strong transcription	Adipose Nuclei	Adipose
11	chr1:156201600-156212800	Strong transcription	Stomach Smooth Muscle	stomach
12	chr1:156201600-156213000	Strong transcription	Fetal Muscle Trunk	muscle
13	chr1:156201600-156213600	Strong transcription	Brain Germinal Matrix	brain
14	chr1:156201600-156213800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr1:156203000-156212800	Strong transcription	Thymus	Thymus
16	chr1:156203200-156212200	Strong transcription	Cortex derived primary cultured neurospheres	brain
17	chr1:156203200-156212400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr1:156203200-156212600	Strong transcription	Primary neutrophils fromperipheralblood	blood
19	chr1:156203400-156212000	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr1:156203400-156212800	Strong transcription	Skeletal Muscle Male	skeletal muscle
21	chr1:156203600-156212200	Strong transcription	Sigmoid Colon	Sigmoid Colon
22	chr1:156203600-156212600	Strong transcription	Left Ventricle	heart
23	chr1:156203600-156212600	Strong transcription	Pancreas	Pancrea
24	chr1:156203800-156213000	Strong transcription	Gastric	stomach
25	chr1:156203800-156213800	Strong transcription	Fetal Intestine Large	intestine
26	chr1:156203800-156214000	Strong transcription	Fetal Intestine Small	intestine
27	chr1:156205600-156212800	Strong transcription	Right Ventricle	heart
28	chr1:156205600-156213000	Strong transcription	Fetal Brain Female	brain
29	chr1:156206800-156215000	Weak transcription	HUVEC	blood vessel
30	chr1:156207800-156212000	Strong transcription	Placenta Amnion	Placenta Amnion
31	chr1:156208000-156214000	Weak transcription	Fetal Kidney	kidney
32	chr1:156208000-156215800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr1:156208200-156214800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
34	chr1:156208200-156220000	Weak transcription	K562	blood
35	chr1:156208400-156215000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
36	chr1:156208400-156215400	Weak transcription	Pancreatic Islets	Pancreatic Islet
37	chr1:156208600-156214000	Weak transcription	Psoas Muscle	Psoas
38	chr1:156208600-156215000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr1:156208800-156212800	Strong transcription	Lung	lung
40	chr1:156209200-156214800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
41	chr1:156209600-156213800	Weak transcription	Rectal Smooth Muscle	rectum
42	chr1:156209600-156214000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr1:156209600-156214200	Weak transcription	Fetal Lung	lung
44	chr1:156209600-156214600	Weak transcription	Small Intestine	intestine
45	chr1:156209600-156215000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr1:156209600-156215000	Weak transcription	HepG2	liver
47	chr1:156209600-156216400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr1:156209600-156216400	Weak transcription	Hela-S3	cervix
49	chr1:156209800-156212600	Weak transcription	Brain Angular Gyrus	brain
50	chr1:156209800-156214000	Weak transcription	Fetal Thymus	thymus

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links