Variant report

Variant	rs1892196
Chromosome Location	chr1:151193897-151193898
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:151177242..151178912-chr1:151193662..151196326,2	MCF-7	breast:
2	chr1:151170945..151172451-chr1:151191867..151194052,2	MCF-7	breast:
3	1:151180715-151199990..1:151402394-151411623	GM12878	blood:
4	chr1:151193469..151196103-chr1:151219484..151222330,2	K562	blood:

Variant related genes	Relation type
ENSG00000143398	Chromatin interaction
ENSG00000238711	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs1056847	0.83[GIH][hapmap];0.81[JPT][hapmap]
rs10749660	0.81[ASW][hapmap];0.95[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.84[LWK][hapmap];0.91[MEX][hapmap];0.86[MKK][hapmap];0.97[TSI][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10788803	0.90[CHB][hapmap];0.83[CHD][hapmap];0.85[GIH][hapmap];0.81[JPT][hapmap];0.80[ASN][1000 genomes]
rs10888406	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10888408	0.94[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];0.90[LWK][hapmap];0.95[MEX][hapmap];0.98[MKK][hapmap];0.92[TSI][hapmap];0.93[YRI][hapmap];0.83[AFR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10888409	0.90[CHB][hapmap];0.83[CHD][hapmap];0.83[GIH][hapmap];0.81[JPT][hapmap]
rs10888410	0.86[CHB][hapmap];0.83[CHD][hapmap];0.83[GIH][hapmap];0.81[JPT][hapmap]
rs11204785	0.90[CHB][hapmap];0.88[CHD][hapmap];0.92[GIH][hapmap];0.86[JPT][hapmap];0.92[TSI][hapmap];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11204791	0.81[ASW][hapmap];0.91[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];0.91[MEX][hapmap];0.86[MKK][hapmap];0.92[TSI][hapmap];0.86[YRI][hapmap];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11204795	0.85[ASN][1000 genomes]
rs11807075	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12022732	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12040384	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12048670	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12062719	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12080778	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12407426	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16827941	0.95[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16833079	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2275900	0.81[ASW][hapmap];0.91[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];0.91[MEX][hapmap];0.86[MKK][hapmap];0.92[TSI][hapmap];0.86[YRI][hapmap];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3811405	0.85[GIH][hapmap]
rs41302131	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4246525	0.86[CHB][hapmap];0.88[CHD][hapmap];0.85[GIH][hapmap]
rs4291501	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4520422	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]
rs4636463	0.90[GIH][hapmap]
rs4970944	0.81[CEU][hapmap];0.90[CHB][hapmap];0.88[CHD][hapmap];0.90[GIH][hapmap];0.86[JPT][hapmap];0.89[TSI][hapmap];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4970948	0.86[CHB][hapmap];0.83[CHD][hapmap];0.80[GIH][hapmap];0.81[JPT][hapmap]
rs4971013	0.95[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4971015	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4971016	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4971021	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4971023	0.95[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4971025	0.81[AFR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4971026	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4971027	0.86[CHB][hapmap];0.85[CHD][hapmap];0.83[GIH][hapmap];0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs4971030	0.86[CHB][hapmap];0.83[CHD][hapmap];0.82[GIH][hapmap];0.81[JPT][hapmap]
rs5022636	0.80[GIH][hapmap]
rs58323986	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61817972	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6587559	0.95[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6587562	0.91[CEU][hapmap];0.86[CHB][hapmap];0.90[CHD][hapmap];0.85[GIH][hapmap];0.81[JPT][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6681071	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6681163	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6683396	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6686402	0.95[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];0.86[MKK][hapmap];0.97[TSI][hapmap];0.80[YRI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6695344	0.94[ASW][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.82[JPT][hapmap];0.98[LWK][hapmap];0.86[MEX][hapmap];0.98[MKK][hapmap];0.87[TSI][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6701325	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7521064	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7527032	0.95[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];0.86[MKK][hapmap];0.97[TSI][hapmap];0.80[YRI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7532935	0.95[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];0.81[MKK][hapmap];0.97[TSI][hapmap];0.80[YRI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7539584	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];1.00[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7544947	0.95[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7552906	0.81[JPT][hapmap]
rs943637	0.86[CHB][hapmap];0.83[CHD][hapmap];0.80[GIH][hapmap];0.85[JPT][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:11)

SNP	Gene	Cis/trans	Tissue	Source
rs1892196	PSMD4	cis	parietal	SCAN
rs1892196	MRPS21	cis	parietal	SCAN
rs1892196	MCL1	cis	lymphoblastoid	seeQTL
rs1892196	SELENBP1	cis	cerebellum	SCAN
rs1892196	CTSS	cis	cerebellum	SCAN
rs1892196	FLG	cis	cerebellum	SCAN
rs1892196	PSMD4	cis	cerebellum	SCAN
rs1892196	ARNT	cis	parietal	SCAN
rs1892196	GPR172A	trans	parietal	SCAN
rs1892196	ANKRD34A	cis	cerebellum	SCAN
rs1892196	HORMAD1	cis	parietal	SCAN

Chromatin state (count:126 , 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	chr1:151173200-151196600	Weak transcription	K562	blood
4	chr1:151173200-151197000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr1:151173200-151199600	Weak transcription	Rectal Smooth Muscle	rectum
6	chr1:151173200-151200000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr1:151173200-151212000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr1:151173200-151227200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr1:151173600-151210600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr1:151174000-151194600	Weak transcription	Brain Substantia Nigra	brain
11	chr1:151174000-151199400	Weak transcription	Small Intestine	intestine
12	chr1:151174200-151200600	Weak transcription	Pancreas	Pancrea
13	chr1:151174400-151203800	Weak transcription	Fetal Brain Male	brain
14	chr1:151175800-151199800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr1:151175800-151200400	Weak transcription	Aorta	Aorta
16	chr1:151176000-151194600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr1:151176200-151200400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr1:151176600-151196400	Weak transcription	Primary B cells from cord blood	blood
19	chr1:151176600-151197000	Weak transcription	Brain Cingulate Gyrus	brain
20	chr1:151178200-151223400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr1:151179600-151197600	Weak transcription	Gastric	stomach
22	chr1:151180000-151196600	Weak transcription	Colonic Mucosa	Colon
23	chr1:151180200-151199800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
24	chr1:151180600-151198000	Weak transcription	Spleen	Spleen
25	chr1:151180800-151194600	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr1:151180800-151197200	Weak transcription	Ovary	ovary
27	chr1:151180800-151199800	Weak transcription	Esophagus	oesophagus
28	chr1:151180800-151206200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
29	chr1:151181000-151194600	Weak transcription	HSMMtube	muscle
30	chr1:151181200-151197200	Weak transcription	Right Ventricle	heart
31	chr1:151181200-151200200	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr1:151181200-151203000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr1:151182400-151199600	Weak transcription	Rectal Mucosa Donor 31	rectum
34	chr1:151182600-151196400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr1:151183400-151199800	Weak transcription	Brain Angular Gyrus	brain
36	chr1:151183600-151194400	Weak transcription	Adipose Nuclei	Adipose
37	chr1:151183600-151196200	Weak transcription	H1 Cell Line	embryonic stem cell
38	chr1:151183600-151197000	Weak transcription	Fetal Lung	lung
39	chr1:151183800-151194600	Weak transcription	Liver	Liver
40	chr1:151183800-151194800	Weak transcription	Brain Hippocampus Middle	brain
41	chr1:151183800-151195000	Weak transcription	Thymus	Thymus
42	chr1:151183800-151196600	Weak transcription	Brain Germinal Matrix	brain
43	chr1:151183800-151196600	Weak transcription	Fetal Brain Female	brain
44	chr1:151184000-151194200	Weak transcription	Left Ventricle	heart
45	chr1:151185000-151194200	Weak transcription	Cortex derived primary cultured neurospheres	brain
46	chr1:151185000-151195000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr1:151185000-151195000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr1:151185000-151196800	Weak transcription	Primary neutrophils fromperipheralblood	blood
49	chr1:151185000-151199400	Weak transcription	HMEC	breast
50	chr1:151185200-151194800	Weak transcription	Colon Smooth Muscle	Colon

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