Variant report

Variant	rs10749660
Chromosome Location	chr1:151174772-151174773
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:21)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:21 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	1:151171193-151178589..1:151411623-151426875	GM12878	blood:
2	chr1:151162248..151163935-chr1:151173326..151176072,2	K562	blood:
3	1:151171193-151178589..1:151246650-151254384	GM12878	blood:
4	chr1:151169497..151174843-chr1:151224312..151231181,18	MCF-7	breast:
5	chr1:151171256..151175527-chr1:151178181..151182275,7	MCF-7	breast:
6	chr1:151138200..151140251-chr1:151173020..151175658,2	MCF-7	breast:
7	chr1:151174124..151175878-chr1:151177531..151179640,2	K562	blood:
8	1:151171193-151178589..1:151333184-151350267	GM12878	blood:
9	chr1:151171117..151172966-chr1:151174600..151177214,2	K562	blood:
10	1:151171193-151178589..1:151219411-151234038	GM12878	blood:
11	1:151171193-151178589..1:151254384-151268403	Hela-S3	cervix:
12	1:151171193-151178589..1:151516085-151535167	GM12878	blood:
13	1:151171193-151178589..1:151203965-151215310	GM12878	blood:
14	chr1:151169149..151172647-chr1:151174192..151177438,5	MCF-7	breast:
15	1:151171193-151178589..1:151368336-151375897	Hela-S3	cervix:
16	chr1:151170625..151172966-chr1:151173912..151176264,4	K562	blood:
17	1:151171193-151178589..1:151496437-151509688	Hela-S3	cervix:
18	1:151171193-151178589..1:151270864-151283078	K562	blood:
19	chr1:151170794..151172311-chr1:151172927..151175239,2	MCF-7	breast:
20	1:151171193-151178589..1:151618750-151636526	Hela-S3	cervix:
21	1:151171193-151178589..1:151309061-151322694	Hela-S3	cervix:

No data

Variant related genes	Relation type
ENSG00000163159	Chromatin interaction
ENSG00000163155	Chromatin interaction
ENSG00000143367	Chromatin interaction
ENSG00000237976	Chromatin interaction
ENSG00000163156	Chromatin interaction
ENSG00000143398	Chromatin interaction
ENSG00000207606	Chromatin interaction
ENSG00000159377	Chromatin interaction
ENSG00000143376	Chromatin interaction
ENSG00000224645	Chromatin interaction
ENSG00000265753	Chromatin interaction
ENSG00000143442	Chromatin interaction
ENSG00000143390	Chromatin interaction
ENSG00000143373	Chromatin interaction
ENSG00000143375	Chromatin interaction
ENSG00000223861	Chromatin interaction
ENSG00000143416	Chromatin interaction
ENSG00000252840	Chromatin interaction
ENSG00000143393	Chromatin interaction
ENSG00000232671	Chromatin interaction
ENSG00000159352	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs1056847	0.83[GIH][hapmap];0.95[JPT][hapmap]
rs10788801	0.90[JPT][hapmap]
rs10788803	0.85[CHB][hapmap];0.85[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap]
rs10888406	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10888408	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];0.90[YRI][hapmap];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10888409	0.85[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	0.86[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];0.90[ASN][1000 genomes]
rs11204791	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];0.81[AFR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11807075	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12022732	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12040384	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12048670	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12062719	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12080778	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12407426	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1536617	0.85[JPT][hapmap]
rs16827941	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16833079	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1752387	0.81[JPT][hapmap]
rs1892196	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]
rs2025900	0.86[JPT][hapmap]
rs2031797	0.85[JPT][hapmap]
rs2275900	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];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2769268	0.86[JPT][hapmap]
rs2769273	0.86[JPT][hapmap]
rs2800946	0.86[JPT][hapmap]
rs3811405	0.86[GIH][hapmap];0.90[JPT][hapmap]
rs3811406	0.85[JPT][hapmap]
rs41302131	0.91[EUR][1000 genomes];0.84[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	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4520422	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]
rs4636463	0.90[GIH][hapmap];0.85[JPT][hapmap]
rs4970944	0.86[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];0.91[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];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4971015	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4971016	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4971018	0.85[JPT][hapmap]
rs4971021	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4971023	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4971025	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4971026	0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4971027	0.90[CHB][hapmap];0.88[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap]
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];0.86[JPT][hapmap];0.81[MEX][hapmap]
rs58323986	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61817972	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[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];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[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];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6678528	0.90[JPT][hapmap]
rs6681071	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6681163	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6683396	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[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];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6695344	0.88[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.85[LWK][hapmap];0.91[MEX][hapmap];0.88[MKK][hapmap];0.89[TSI][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6701325	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7521064	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[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];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[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];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7539584	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];0.86[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[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];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[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
rs10749660	MRPS21	cis	parietal	SCAN
rs10749660	PSMD4	cis	cerebellum	SCAN
rs10749660	CTSS	cis	cerebellum	SCAN
rs10749660	FLG	cis	cerebellum	SCAN
rs10749660	PSMD4	cis	parietal	SCAN
rs10749660	ARNT	cis	parietal	SCAN
rs10749660	ANKRD34A	cis	cerebellum	SCAN
rs10749660	SELENBP1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151172600-151174800	Enhancers	Primary monocytes fromperipheralblood	blood
2	chr1:151172800-151175000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
3	chr1:151172800-151175000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
4	chr1:151172800-151175000	Enhancers	Colon Smooth Muscle	Colon
5	chr1:151172800-151175400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr1:151172800-151179000	Weak transcription	Gastric	stomach
7	chr1:151172800-151197200	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr1:151172800-151204400	Weak transcription	Stomach Mucosa	stomach
9	chr1:151173000-151174800	Enhancers	Rectal Mucosa Donor 31	rectum
10	chr1:151173000-151175200	Weak transcription	Esophagus	oesophagus
11	chr1:151173200-151174800	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr1:151173200-151174800	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr1:151173200-151174800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr1:151173200-151174800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
15	chr1:151173200-151175000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr1:151173200-151175000	Enhancers	Adipose Nuclei	Adipose
17	chr1:151173200-151175000	Weak transcription	Fetal Muscle Leg	muscle
18	chr1:151173200-151175000	Enhancers	Skeletal Muscle Female	skeletal muscle
19	chr1:151173200-151175200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr1:151173200-151175200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr1:151173200-151175200	Weak transcription	Primary neutrophils fromperipheralblood	blood
22	chr1:151173200-151175200	Weak transcription	Aorta	Aorta
23	chr1:151173200-151175200	Enhancers	Skeletal Muscle Male	skeletal muscle
24	chr1:151173200-151178400	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr1:151173200-151179200	Weak transcription	Right Atrium	heart
26	chr1:151173200-151179400	Weak transcription	Fetal Brain Female	brain
27	chr1:151173200-151182200	Weak transcription	Brain Angular Gyrus	brain
28	chr1:151173200-151191600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr1:151173200-151196600	Weak transcription	K562	blood
30	chr1:151173200-151197000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr1:151173200-151199600	Weak transcription	Rectal Smooth Muscle	rectum
32	chr1:151173200-151200000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr1:151173200-151212000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr1:151173200-151227200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr1:151173400-151174800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
36	chr1:151173400-151175200	Enhancers	HUVEC	blood vessel
37	chr1:151173600-151210600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr1:151173800-151174800	Genic enhancers	A549	lung
39	chr1:151173800-151175000	Genic enhancers	Primary T helper cells fromperipheralblood	blood
40	chr1:151173800-151175200	Enhancers	Psoas Muscle	Psoas
41	chr1:151173800-151175400	Enhancers	Primary hematopoietic stem cells	blood
42	chr1:151173800-151175400	Weak transcription	Brain Germinal Matrix	brain
43	chr1:151173800-151175400	Weak transcription	Fetal Kidney	kidney
44	chr1:151173800-151185200	Strong transcription	Fetal Intestine Small	intestine
45	chr1:151174000-151174800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr1:151174000-151174800	Weak transcription	Brain Cingulate Gyrus	brain
47	chr1:151174000-151174800	Enhancers	Colonic Mucosa	Colon
48	chr1:151174000-151174800	Weak transcription	Thymus	Thymus
49	chr1:151174000-151174800	Enhancers	Monocytes-CD14+_RO01746	blood
50	chr1:151174000-151175000	Weak transcription	HSMM	muscle

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