Variant report

Variant	rs2273936
Chromosome Location	chr1:227920925-227920926
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:11)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:11 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:227914982-227921463	K562	blood:	n/a	n/a
2	POLR2A	chr1:227920367-227920960	HL-60	blood:	n/a	n/a
3	POLR2A	chr1:227915700-227921841	GM12878	blood:	n/a	n/a
4	POLR2A	chr1:227914208-227920934	K562	blood:	n/a	n/a
5	POLR2A	chr1:227920345-227921869	GM12878	blood:	n/a	n/a
6	POLR2A	chr1:227915660-227921896	HepG2	liver:	n/a	n/a
7	POLR2A	chr1:227920356-227921037	H1-hESC	embryonic stem cell:	n/a	n/a
8	POLR2A	chr1:227915672-227920956	HEK293	kidney:	n/a	n/a
9	POLR2A	chr1:227916255-227921984	K562	blood:	n/a	n/a
10	POLR2A	chr1:227916827-227921915	GM12878	blood:	n/a	n/a
11	POLR2A	chr1:227916248-227922017	SK-N-MC	brain:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:227917727..227921370-chr1:227944241..227947517,4	MCF-7	breast:
2	chr1:227918805..227924684-chr1:227929963..227939883,12	K562	blood:
3	chr1:227754198..227755750-chr1:227920040..227921876,2	K562	blood:
4	chr1:227672982..227674850-chr1:227918666..227921281,2	MCF-7	breast:
5	chr1:227919994..227921711-chr6:43019722..43021797,2	MCF-7	breast:
6	chr1:227916221..227923035-chr1:228131852..228141791,18	MCF-7	breast:

No data

Variant related genes	Relation type
SNAP47	TF binding region
ENSG00000044090	Chromatin interaction
ENSG00000143816	Chromatin interaction
ENSG00000230005	Chromatin interaction
ENSG00000143740	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs12566948	0.89[CEU][hapmap]
rs1570429	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16848110	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs17851681	0.88[CEU][hapmap];0.83[CHD][hapmap];0.91[GIH][hapmap];0.88[JPT][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2029836	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2031132	0.81[CEU][hapmap]
rs3806264	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41270161	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41270167	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4837	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58565844	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs748405	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534002	chr1:227315186-228047108	Bivalent/Poised TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
2	nsv1007479	chr1:227695868-227984466	Genic enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
3	nsv1010605	chr1:227770415-228332690	Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
4	esv32853	chr1:227880116-228806209	Enhancers Genic enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	187 gene(s)	inside rSNPs	diseases
5	nsv427952	chr1:227881664-228308629	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
6	nsv826908	chr1:227895386-228691100	Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
7	nsv515496	chr1:227912474-227967938	Active TSS Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
8	esv3387540	chr1:227919379-227922177	Enhancers Genic enhancers Flanking Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	n/a
9	nsv873249	chr1:227920061-228121548	Weak transcription Bivalent Enhancer Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2273936	ZNF678	cis	Muscle Skeletal	GTEx
rs2273936	HIST3H2A	cis	parietal	SCAN
rs2273936	HIST3H2A	cis	cerebellum	SCAN
rs2273936	C1orf142	Cis_1M	lymphoblastoid	RTeQTL
rs2273936	C1orf35	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227916800-227921600	Weak transcription	HUVEC	blood vessel
2	chr1:227917000-227921000	Weak transcription	Hela-S3	cervix
3	chr1:227917000-227921800	Weak transcription	Primary hematopoietic stem cells	blood
4	chr1:227917000-227921800	Weak transcription	Psoas Muscle	Psoas
5	chr1:227917200-227921400	Weak transcription	Fetal Brain Male	brain
6	chr1:227917200-227921400	Weak transcription	NH-A	brain
7	chr1:227917200-227921600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr1:227917200-227921600	Weak transcription	Stomach Mucosa	stomach
9	chr1:227917200-227922000	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr1:227917400-227921400	Weak transcription	Primary B cells from cord blood	blood
11	chr1:227917400-227921400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr1:227917600-227921400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr1:227917800-227921400	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr1:227918000-227921600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr1:227918200-227921200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr1:227918200-227921800	Genic enhancers	Fetal Muscle Leg	muscle
17	chr1:227918400-227921000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr1:227918400-227921200	Strong transcription	Fetal Stomach	stomach
19	chr1:227918400-227921200	Strong transcription	Thymus	Thymus
20	chr1:227918400-227921800	Genic enhancers	Fetal Muscle Trunk	muscle
21	chr1:227918400-227922000	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr1:227918600-227921000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr1:227918600-227921000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
24	chr1:227918600-227921000	Strong transcription	Esophagus	oesophagus
25	chr1:227918600-227921200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr1:227918600-227921200	Strong transcription	HSMMtube	muscle
27	chr1:227918600-227921200	Strong transcription	NHEK	skin
28	chr1:227918600-227921400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr1:227918600-227921400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr1:227918600-227921400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr1:227918600-227921400	Strong transcription	Cortex derived primary cultured neurospheres	brain
32	chr1:227918600-227921400	Strong transcription	K562	blood
33	chr1:227918600-227921400	Strong transcription	NHLF	lung
34	chr1:227918600-227921600	Weak transcription	Right Atrium	heart
35	chr1:227918600-227921600	Strong transcription	A549	lung
36	chr1:227918600-227921600	Weak transcription	HSMM	muscle
37	chr1:227918600-227922000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
38	chr1:227918600-227922000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
39	chr1:227918800-227921000	Strong transcription	Primary T cells fromperipheralblood	blood
40	chr1:227918800-227921000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
41	chr1:227918800-227921000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr1:227918800-227921000	Strong transcription	Adipose Nuclei	Adipose
43	chr1:227918800-227921000	Strong transcription	Skeletal Muscle Female	skeletal muscle
44	chr1:227918800-227921000	Strong transcription	HMEC	breast
45	chr1:227918800-227921200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr1:227918800-227921200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr1:227918800-227921200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr1:227918800-227921200	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
49	chr1:227918800-227921400	Strong transcription	Brain Anterior Caudate	brain
50	chr1:227918800-227921400	Strong transcription	Brain Substantia Nigra	brain

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