Variant report

Variant	rs1570429
Chromosome Location	chr1:227917645-227917646
allele	C/T
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:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:227675888..227678254-chr1:227916925..227919075,2	MCF-7	breast:
2	chr1:227916462..227918009-chr11:796491..798372,2	MCF-7	breast:
3	chr1:227916806..227918917-chr16:56965521..56967737,2	K562	blood:
4	chr1:227916734..227919516-chr1:228336405..228338652,2	MCF-7	breast:
5	chr1:227916288..227917792-chr1:227932623..227935322,2	K562	blood:
6	chr1:227669242..227673785-chr1:227914780..227918377,5	MCF-7	breast:
7	chr1:227917049..227918817-chr17:57920082..57922473,2	MCF-7	breast:
8	chr1:227916348..227918529-chr1:228270679..228272482,2	MCF-7	breast:
9	chr1:227917332..227919263-chr20:52209333..52211800,2	MCF-7	breast:
10	chr1:227917409..227918706-chr1:228134035..228134836,3	MCF-7	breast:
11	chr1:227915693..227918216-chr1:228290174..228292173,2	MCF-7	breast:
12	chr1:227916225..227917863-chr2:32234372..32236417,2	MCF-7	breast:
13	chr1:227915024..227917795-chr17:57915230..57917196,2	MCF-7	breast:
14	chr1:227916221..227923035-chr1:228131852..228141791,18	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000143816	Chromatin interaction
ENSG00000062716	Chromatin interaction
ENSG00000177542	Chromatin interaction
ENSG00000143761	Chromatin interaction
ENSG00000230005	Chromatin interaction
ENSG00000162959	Chromatin interaction
ENSG00000198835	Chromatin interaction
ENSG00000143793	Chromatin interaction
ENSG00000171940	Chromatin interaction
ENSG00000051108	Chromatin interaction
ENSG00000237193	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs12566948	0.89[CEU][hapmap]
rs16848110	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.96[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];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]
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];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3806264	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]
rs41270161	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41270167	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4837	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58565844	0.90[AFR][1000 genomes];1.00[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];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]

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	nsv945344	chr1:227899939-227917776	Active TSS Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	18 gene(s)	inside rSNPs	diseases
8	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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1570429	HIST3H2A	cis	parietal	SCAN
rs1570429	C1orf35	cis	parietal	SCAN
rs1570429	HIST3H2A	cis	cerebellum	SCAN
rs1570429	C1orf142	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227916200-227918600	Weak transcription	HSMMtube	muscle
2	chr1:227916400-227918200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
3	chr1:227916400-227918600	Flanking Active TSS	Stomach Smooth Muscle	stomach
4	chr1:227916600-227918000	Weak transcription	HSMM	muscle
5	chr1:227916600-227919600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr1:227916800-227917800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr1:227916800-227918000	Enhancers	Primary T killer memory cells from peripheral blood	blood
8	chr1:227916800-227918000	Enhancers	Esophagus	oesophagus
9	chr1:227916800-227918200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr1:227916800-227918200	Enhancers	Brain Substantia Nigra	brain
11	chr1:227916800-227918400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr1:227916800-227918400	Enhancers	Gastric	stomach
13	chr1:227916800-227918400	Enhancers	K562	blood
14	chr1:227916800-227918400	Weak transcription	NHLF	lung
15	chr1:227916800-227918600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
16	chr1:227916800-227918600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr1:227916800-227918600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
18	chr1:227916800-227918800	Enhancers	Placenta	Placenta
19	chr1:227916800-227919400	Weak transcription	Aorta	Aorta
20	chr1:227916800-227919400	Weak transcription	Osteobl	bone
21	chr1:227916800-227921600	Weak transcription	HUVEC	blood vessel
22	chr1:227917000-227917800	Enhancers	Primary B cells from peripheral blood	blood
23	chr1:227917000-227917800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr1:227917000-227917800	Enhancers	Duodenum Mucosa	Duodenum
25	chr1:227917000-227918000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr1:227917000-227918000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr1:227917000-227918000	Enhancers	Brain Angular Gyrus	brain
28	chr1:227917000-227918200	Enhancers	Primary T helper cells PMA-I stimulated	--
29	chr1:227917000-227918200	Enhancers	Fetal Muscle Leg	muscle
30	chr1:227917000-227918200	Enhancers	Fetal Stomach	stomach
31	chr1:227917000-227918200	Enhancers	Fetal Thymus	thymus
32	chr1:227917000-227918400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr1:227917000-227918400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
34	chr1:227917000-227918400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
35	chr1:227917000-227918400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr1:227917000-227918400	Enhancers	Brain Hippocampus Middle	brain
37	chr1:227917000-227918400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
38	chr1:227917000-227918400	Enhancers	Fetal Intestine Small	intestine
39	chr1:227917000-227918400	Enhancers	Fetal Lung	lung
40	chr1:227917000-227918400	Enhancers	Fetal Muscle Trunk	muscle
41	chr1:227917000-227918400	Enhancers	HepG2	liver
42	chr1:227917000-227918600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr1:227917000-227918600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr1:227917000-227918600	Enhancers	Primary T cells fromperipheralblood	blood
45	chr1:227917000-227918600	Weak transcription	Cortex derived primary cultured neurospheres	brain
46	chr1:227917000-227918600	Enhancers	Adipose Nuclei	Adipose
47	chr1:227917000-227918600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
48	chr1:227917000-227918600	Enhancers	Right Atrium	heart
49	chr1:227917000-227918600	Enhancers	Right Ventricle	heart
50	chr1:227917000-227918600	Weak transcription	NHEK	skin

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