Variant report

Variant	rs3806264
Chromosome Location	chr1:227925103-227925104
allele	C/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	POLR2A	chr1:227924941-227925151	MCF10A-Er-Src	breast:	n/a	n/a
2	ZNF263	chr1:227924525-227925651	HEK293-T-REx	kidney:	n/a	chr1:227925421-227925442 chr1:227925381-227925390
3	POLR2A	chr1:227925023-227925109	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:227924900..227928160-chr1:227933336..227936259,3	K562	blood:
2	chr1:227924939..227926521-chr1:227948276..227949805,2	MCF-7	breast:
3	chr1:227923000..227925656-chr1:228268639..228271303,2	MCF-7	breast:

Variant related genes	Relation type
JMJD4	TF binding region
ENSG00000230005	Chromatin interaction
ENSG00000143740	Chromatin interaction
ENSG00000143761	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs12566948	0.89[CEU][hapmap]
rs1570429	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16848110	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes]
rs17851681	0.88[CEU][hapmap];0.83[CHD][hapmap];0.91[GIH][hapmap];0.89[JPT][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[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];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2031132	0.81[CEU][hapmap]
rs2273936	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	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41270167	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41305134	0.81[EUR][1000 genomes]
rs4837	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58565844	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs748405	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7543525	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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	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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3806264	C1orf35	cis	parietal	SCAN
rs3806264	HIST3H2A	cis	parietal	SCAN
rs3806264	HIST3H2A	cis	cerebellum	SCAN
rs3806264	C1orf142	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227923600-227925200	Flanking Active TSS	Dnd41	blood
2	chr1:227923800-227935600	Weak transcription	Aorta	Aorta
3	chr1:227924000-227925200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr1:227924000-227925200	Enhancers	Fetal Stomach	stomach
5	chr1:227924000-227925200	Enhancers	Psoas Muscle	Psoas
6	chr1:227924000-227925200	Weak transcription	Small Intestine	intestine
7	chr1:227924000-227925400	Enhancers	Primary T cells fromperipheralblood	blood
8	chr1:227924000-227925400	Enhancers	Left Ventricle	heart
9	chr1:227924000-227925400	Enhancers	Pancreas	Pancrea
10	chr1:227924000-227925600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr1:227924000-227928200	Weak transcription	Right Atrium	heart
12	chr1:227924000-227932000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr1:227924000-227935400	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr1:227924000-227935600	Weak transcription	Monocytes-CD14+_RO01746	blood
15	chr1:227924000-227936400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr1:227924200-227925200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr1:227924200-227925200	Enhancers	Brain Inferior Temporal Lobe	brain
18	chr1:227924200-227925200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
19	chr1:227924200-227925200	Enhancers	Duodenum Smooth Muscle	Duodenum
20	chr1:227924200-227925200	Enhancers	HepG2	liver
21	chr1:227924200-227925400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr1:227924200-227925400	Enhancers	Brain Angular Gyrus	brain
23	chr1:227924200-227925600	Enhancers	Breast Myoepithelial Primary Cells	Breast
24	chr1:227924200-227925600	Enhancers	Fetal Brain Female	brain
25	chr1:227924200-227925600	Enhancers	Ovary	ovary
26	chr1:227924200-227925600	Enhancers	Skeletal Muscle Female	skeletal muscle
27	chr1:227924200-227925600	Enhancers	GM12878-XiMat	blood
28	chr1:227924200-227926200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr1:227924200-227926600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr1:227924200-227927000	Weak transcription	Fetal Intestine Large	intestine
31	chr1:227924200-227927000	Weak transcription	Spleen	Spleen
32	chr1:227924200-227927400	Weak transcription	Gastric	stomach
33	chr1:227924200-227927600	Weak transcription	Rectal Mucosa Donor 31	rectum
34	chr1:227924200-227930800	Weak transcription	NHEK	skin
35	chr1:227924200-227931200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
36	chr1:227924200-227931600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
37	chr1:227924200-227931600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
38	chr1:227924200-227931800	Weak transcription	Duodenum Mucosa	Duodenum
39	chr1:227924200-227932000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr1:227924200-227932400	Weak transcription	Fetal Thymus	thymus
41	chr1:227924200-227933800	Weak transcription	Primary neutrophils fromperipheralblood	blood
42	chr1:227924200-227933800	Weak transcription	HMEC	breast
43	chr1:227924200-227934600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr1:227924200-227934800	Weak transcription	HUES6 Cell Line	embryonic stem cell
45	chr1:227924200-227935000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
46	chr1:227924200-227935000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr1:227924200-227935000	Weak transcription	Rectal Smooth Muscle	rectum
48	chr1:227924200-227935400	Weak transcription	H1 Cell Line	embryonic stem cell
49	chr1:227924200-227935400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr1:227924200-227935400	Weak transcription	H9 Cell Line	embryonic stem cell

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