Variant report

Variant	rs4520422
Chromosome Location	chr1:151179943-151179944
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:151171256..151175527-chr1:151178181..151182275,7	MCF-7	breast:
2	1:151178589-151180715..1:151246650-151254384	GM12878	blood:
3	chr1:151175695..151178568-chr1:151178857..151183674,4	MCF-7	breast:
4	chr1:151171022..151173926-chr1:151179427..151183184,4	K562	blood:
5	chr1:151177346..151179948-chr1:151225610..151227911,2	K562	blood:
6	1:151178589-151180715..1:151219411-151234038	GM12878	blood:

Variant related genes	Relation type
ENSG00000159352	Chromatin interaction
ENSG00000232671	Chromatin interaction
ENSG00000143373	Chromatin interaction
ENSG00000143398	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs1056847	0.83[GIH][hapmap];0.95[JPT][hapmap]
rs10749660	0.88[ASW][hapmap];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];0.88[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10788801	0.90[JPT][hapmap]
rs10788803	0.84[CHB][hapmap];0.85[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap]
rs10888406	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10888408	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.94[TSI][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10888409	0.84[CHB][hapmap];0.85[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap]
rs10888410	0.90[CHB][hapmap];0.85[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap]
rs11204785	0.82[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.94[TSI][hapmap];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11204791	0.88[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.94[TSI][hapmap];0.89[YRI][hapmap];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11204795	0.82[ASN][1000 genomes]
rs11807075	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12022732	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12040384	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12048670	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12062719	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12080778	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12407426	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1536617	0.85[JPT][hapmap]
rs16827941	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16833079	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1892196	0.94[ASW][hapmap];0.95[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.98[LWK][hapmap];0.91[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2025900	0.85[JPT][hapmap]
rs2031797	0.85[JPT][hapmap]
rs2275900	0.88[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.94[TSI][hapmap];0.89[YRI][hapmap];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2769267	0.81[JPT][hapmap]
rs2769268	0.85[JPT][hapmap]
rs2769273	0.85[JPT][hapmap]
rs2800946	0.85[JPT][hapmap]
rs3811405	0.86[GIH][hapmap];0.90[JPT][hapmap]
rs3811406	0.85[JPT][hapmap]
rs41302131	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4246525	0.90[CHB][hapmap];0.90[CHD][hapmap];0.86[GIH][hapmap];0.90[JPT][hapmap];0.82[MEX][hapmap]
rs4291501	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4636463	0.90[GIH][hapmap];0.84[JPT][hapmap]
rs4970944	0.82[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.92[TSI][hapmap];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4970948	0.90[CHB][hapmap];0.85[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap]
rs4971013	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4971015	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4971016	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4971018	0.85[JPT][hapmap]
rs4971021	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4971023	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4971025	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4971026	0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4971027	0.90[CHB][hapmap];0.88[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.82[ASN][1000 genomes]
rs4971029	0.85[JPT][hapmap]
rs4971030	0.90[CHB][hapmap];0.85[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap]
rs5022636	0.81[GIH][hapmap];0.85[JPT][hapmap];0.81[MEX][hapmap]
rs58323986	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61817972	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6587559	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6587562	0.95[CEU][hapmap];0.90[CHB][hapmap];0.92[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6678528	0.90[JPT][hapmap]
rs6681071	0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6681163	0.82[AFR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6683396	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6686402	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6695344	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6701325	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7521064	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7527032	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7532935	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7539584	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7544947	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7545392	0.90[JPT][hapmap]
rs7552906	0.86[JPT][hapmap]
rs943637	0.90[CHB][hapmap];0.85[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.81[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001897	chr1:150743271-151241600	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
2	nsv535158	chr1:150743271-151241600	Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
3	nsv522840	chr1:150933723-151347746	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	169 gene(s)	inside rSNPs	diseases
4	nsv916272	chr1:150961809-151557253	Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	219 gene(s)	inside rSNPs	diseases
5	nsv831559	chr1:151109459-151239921	Active TSS Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
6	nsv831570	chr1:151129020-151281778	Strong transcription Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	106 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs4520422	FLG	cis	cerebellum	SCAN
rs4520422	PSMD4	cis	parietal	SCAN
rs4520422	MRPS21	cis	parietal	SCAN
rs4520422	PSMD4	cis	cerebellum	SCAN
rs4520422	SELENBP1	cis	cerebellum	SCAN
rs4520422	CTSS	cis	cerebellum	SCAN
rs4520422	ANKRD34A	cis	cerebellum	SCAN
rs4520422	ARNT	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151172800-151197200	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr1:151172800-151204400	Weak transcription	Stomach Mucosa	stomach
3	chr1:151173200-151182200	Weak transcription	Brain Angular Gyrus	brain
4	chr1:151173200-151191600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr1:151173200-151196600	Weak transcription	K562	blood
6	chr1:151173200-151197000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr1:151173200-151199600	Weak transcription	Rectal Smooth Muscle	rectum
8	chr1:151173200-151200000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr1:151173200-151212000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr1:151173200-151227200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr1:151173600-151210600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr1:151173800-151185200	Strong transcription	Fetal Intestine Small	intestine
13	chr1:151174000-151194600	Weak transcription	Brain Substantia Nigra	brain
14	chr1:151174000-151199400	Weak transcription	Small Intestine	intestine
15	chr1:151174200-151200600	Weak transcription	Pancreas	Pancrea
16	chr1:151174400-151180800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
17	chr1:151174400-151183600	Strong transcription	Fetal Thymus	thymus
18	chr1:151174400-151183800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr1:151174400-151187000	Strong transcription	HUES48 Cell Line	embryonic stem cell
20	chr1:151174400-151189200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr1:151174400-151203800	Weak transcription	Fetal Brain Male	brain
22	chr1:151174600-151184400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
23	chr1:151174600-151185000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr1:151174600-151185200	Strong transcription	Fetal Muscle Trunk	muscle
25	chr1:151174800-151180400	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr1:151174800-151181800	Strong transcription	A549	lung
27	chr1:151174800-151183600	Strong transcription	Primary T cells from cord blood	blood
28	chr1:151175000-151180800	Strong transcription	Primary B cells from peripheral blood	blood
29	chr1:151175000-151182800	Strong transcription	NHEK	skin
30	chr1:151175000-151185400	Strong transcription	Fetal Stomach	stomach
31	chr1:151175000-151189000	Weak transcription	Pancreatic Islets	Pancreatic Islet
32	chr1:151175200-151184000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr1:151175200-151185200	Weak transcription	Psoas Muscle	Psoas
34	chr1:151175400-151183400	Weak transcription	Primary hematopoietic stem cells	blood
35	chr1:151175600-151182800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr1:151175600-151185000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
37	chr1:151175800-151180000	Weak transcription	Adipose Nuclei	Adipose
38	chr1:151175800-151180200	Weak transcription	Fetal Kidney	kidney
39	chr1:151175800-151183200	Weak transcription	NH-A	brain
40	chr1:151175800-151193800	Weak transcription	Skeletal Muscle Female	skeletal muscle
41	chr1:151175800-151199800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr1:151175800-151200400	Weak transcription	Aorta	Aorta
43	chr1:151176000-151194600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
44	chr1:151176200-151180000	Weak transcription	Brain Anterior Caudate	brain
45	chr1:151176200-151200400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
46	chr1:151176600-151196400	Weak transcription	Primary B cells from cord blood	blood
47	chr1:151176600-151197000	Weak transcription	Brain Cingulate Gyrus	brain
48	chr1:151177000-151182800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr1:151177200-151183400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
50	chr1:151177400-151181600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links