Variant report

Variant	rs748405
Chromosome Location	chr1:227947434-227947435
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:227946182..227953403-chr1:228132950..228136592,12	MCF-7	breast:
2	chr1:227926788..227928510-chr1:227944634..227947567,2	MCF-7	breast:
3	chr1:227945049..227947627-chr1:228289344..228291070,2	MCF-7	breast:
4	chr1:227946584..227948146-chr1:228139573..228141721,2	MCF-7	breast:
5	chr1:227945386..227947892-chr1:227948405..227951247,3	MCF-7	breast:
6	chr1:227946633..227949211-chr1:228261877..228264518,2	K562	blood:
7	chr1:227938992..227942354-chr1:227946217..227950282,3	K562	blood:
8	chr1:227945350..227947545-chr1:228134619..228136982,2	MCF-7	breast:
9	chr1:227917727..227921370-chr1:227944241..227947517,4	MCF-7	breast:
10	chr1:227920395..227923971-chr1:227944832..227949362,8	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000143816	Chromatin interaction
ENSG00000081692	Chromatin interaction
ENSG00000143740	Chromatin interaction
ENSG00000143793	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 5 )

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

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];0.85[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];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]
rs3806264	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]
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	0.91[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs4837	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58565844	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7543525	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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
9	nsv468238	chr1:227935762-228045748	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
10	nsv549272	chr1:227935762-228045748	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs748405	JMJD4	cis	multi-tissue	Pritchard
rs748405	C1orf142	Cis_1M	lymphoblastoid	RTeQTL
rs748405	HIST3H2A	cis	parietal	SCAN
rs748405	C1orf35	cis	parietal	SCAN
rs748405	HIST3H2A	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227924200-227955000	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr1:227934000-227948800	Strong transcription	Primary T cells from cord blood	blood
3	chr1:227934400-227950000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr1:227934800-227950200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr1:227934800-227950400	Strong transcription	Fetal Intestine Small	intestine
6	chr1:227935000-227949600	Strong transcription	Dnd41	blood
7	chr1:227935200-227949800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr1:227937200-227949600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
9	chr1:227938000-227950200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr1:227938600-227950400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr1:227940400-227950000	Strong transcription	HepG2	liver
12	chr1:227940800-227949800	Strong transcription	Thymus	Thymus
13	chr1:227942000-227950000	Weak transcription	Small Intestine	intestine
14	chr1:227942200-227948600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr1:227942600-227949200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
16	chr1:227942600-227949200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr1:227942600-227950000	Weak transcription	Stomach Mucosa	stomach
18	chr1:227943400-227948400	Enhancers	Psoas Muscle	Psoas
19	chr1:227943400-227949600	Strong transcription	Cortex derived primary cultured neurospheres	brain
20	chr1:227943400-227949800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr1:227943600-227949400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr1:227943600-227949400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
23	chr1:227943600-227949800	Strong transcription	HUES6 Cell Line	embryonic stem cell
24	chr1:227943600-227949800	Strong transcription	Monocytes-CD14+_RO01746	blood
25	chr1:227943800-227948000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr1:227944000-227949800	Strong transcription	Brain Germinal Matrix	brain
27	chr1:227944000-227950400	Strong transcription	Fetal Intestine Large	intestine
28	chr1:227944000-227951800	Genic enhancers	Fetal Muscle Leg	muscle
29	chr1:227944200-227950000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr1:227944400-227947600	Strong transcription	A549	lung
31	chr1:227944400-227949200	Strong transcription	Esophagus	oesophagus
32	chr1:227944400-227949400	Strong transcription	K562	blood
33	chr1:227944400-227949600	Strong transcription	HUES64 Cell Line	embryonic stem cell
34	chr1:227944600-227949800	Weak transcription	Hela-S3	cervix
35	chr1:227944800-227948000	Genic enhancers	Fetal Stomach	stomach
36	chr1:227944800-227948200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr1:227944800-227949400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr1:227944800-227949400	Strong transcription	Spleen	Spleen
39	chr1:227945000-227947800	Strong transcription	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr1:227945000-227949200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
41	chr1:227945000-227949200	Strong transcription	Primary B cells from peripheral blood	blood
42	chr1:227945000-227949400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr1:227945000-227949800	Strong transcription	HUES48 Cell Line	embryonic stem cell
44	chr1:227945400-227948000	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr1:227945400-227948600	Enhancers	Placenta Amnion	Placenta Amnion
46	chr1:227945400-227948800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
47	chr1:227945400-227949600	Strong transcription	Primary B cells from cord blood	blood
48	chr1:227945600-227948400	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr1:227945600-227948400	Strong transcription	Liver	Liver
50	chr1:227945600-227949600	Strong transcription	Brain Substantia Nigra	brain

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