Variant report

Variant	rs7136770
Chromosome Location	chr12:57381259-57381260
allele	G/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:23)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:23 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:57380165..57383091-chr12:57391250..57394280,3	K562	blood:
2	chr12:57156626..57157533-chr12:57381026..57381957,4	MCF-7	breast:
3	chr12:57381112..57381620-chr12:57394915..57395894,2	MCF-7	breast:
4	chr12:57233421..57234366-chr12:57381033..57382023,8	MCF-7	breast:
5	chr12:57326458..57328470-chr12:57381157..57384002,3	MCF-7	breast:
6	chr12:57347827..57349628-chr12:57379616..57381539,3	MCF-7	breast:
7	chr12:57351085..57351674-chr12:57381073..57381575,2	MCF-7	breast:
8	chr12:57232476..57232993-chr12:57380642..57381474,2	MCF-7	breast:
9	chr12:57157055..57157574-chr12:57381025..57381543,2	K562	blood:
10	chr12:57156608..57159061-chr12:57379164..57381627,2	MCF-7	breast:
11	chr12:57233353..57235203-chr12:57380743..57382388,18	MCF-7	breast:
12	chr12:57151018..57151992-chr12:57381056..57381889,5	MCF-7	breast:
13	chr12:57156921..57157570-chr12:57381033..57381981,4	MCF-7	breast:
14	chr12:57349736..57351385-chr12:57380003..57382609,2	MCF-7	breast:
15	chr12:57151005..57151996-chr12:57381006..57381955,2	K562	blood:
16	chr12:57341090..57342031-chr12:57380872..57381968,6	MCF-7	breast:
17	chr12:57381152..57386440-chr12:57387295..57390805,5	K562	blood:
18	chr12:57116564..57119483-chr12:57379649..57381889,2	MCF-7	breast:
19	chr12:57341567..57342147-chr12:57381088..57381948,3	MCF-7	breast:
20	chr12:57232928..57235574-chr12:57379321..57382266,3	MCF-7	breast:
21	chr12:57380979..57383508-chr12:57478377..57480452,2	MCF-7	breast:
22	chr12:57233059..57234536-chr12:57380344..57382025,8	K562	blood:
23	chr12:57023280..57025743-chr12:57378551..57381481,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000076108	Chromatin interaction
ENSG00000170426	Chromatin interaction
ENSG00000025423	Chromatin interaction
ENSG00000268162	Chromatin interaction
ENSG00000258442	Chromatin interaction
ENSG00000166856	Chromatin interaction
ENSG00000196531	Chromatin interaction

Extended variants
information (count: 121 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:116)

rs_ID	r²[population]
rs10400412	0.97[ASN][1000 genomes]
rs10400555	0.97[ASN][1000 genomes]
rs1044939	0.90[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs10506347	0.91[CEU][hapmap];0.97[GIH][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes]
rs10506350	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10506351	0.90[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs1072670	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11172071	0.82[GIH][hapmap]
rs11832487	0.94[ASN][1000 genomes]
rs11834851	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11834856	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11836517	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12099695	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs12810024	0.91[CEU][hapmap];0.90[CHB][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12810837	0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12812221	0.81[GIH][hapmap]
rs12812499	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12815538	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12818342	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12824682	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12827039	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12827286	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1552245	0.90[CHB][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs17119173	0.81[GIH][hapmap]
rs17119301	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];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17119327	0.90[CHB][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs17119330	0.90[CHB][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs17119344	0.90[CHB][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs17119352	0.93[ASN][1000 genomes]
rs17119386	0.90[CHB][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs17119388	0.90[CHB][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs17119390	0.90[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs17119407	0.90[CHB][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs17119416	1.00[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs17119418	1.00[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap]
rs1843311	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1843312	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1843313	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1872436	0.82[GIH][hapmap]
rs2035545	0.86[JPT][hapmap]
rs2167306	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2270736	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2270737	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2270739	0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2279373	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2279743	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2291855	0.90[CHB][hapmap];0.86[JPT][hapmap];0.97[ASN][1000 genomes]
rs2371717	0.90[CHB][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs28589663	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2888139	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3024974	0.92[CHD][hapmap]
rs34186462	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34253098	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34359134	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34762603	0.82[ASN][1000 genomes]
rs34969650	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35034299	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35243318	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35493121	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs3782329	0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs3782330	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs3803018	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs3894415	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4016338	0.90[CHB][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs4039	0.90[CHB][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs4143085	0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs56128678	0.90[ASN][1000 genomes]
rs56270558	0.90[ASN][1000 genomes]
rs56354404	0.90[ASN][1000 genomes]
rs57056392	0.91[ASN][1000 genomes]
rs57129030	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57351760	0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57558853	0.97[ASN][1000 genomes]
rs58298943	1.00[ASN][1000 genomes]
rs58389529	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs60258120	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60273384	0.99[ASN][1000 genomes]
rs60380217	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61504157	0.91[ASN][1000 genomes]
rs67476535	0.99[ASN][1000 genomes]
rs67771054	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs67844278	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs68126184	1.00[ASN][1000 genomes]
rs697222	0.81[CHD][hapmap];0.90[GIH][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs7135297	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs71461303	0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72482268	0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7298475	1.00[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs73114426	0.97[ASN][1000 genomes]
rs73114428	0.97[ASN][1000 genomes]
rs73114434	0.97[ASN][1000 genomes]
rs73114436	0.97[ASN][1000 genomes]
rs73114437	0.93[ASN][1000 genomes]
rs73114446	0.93[ASN][1000 genomes]
rs73114452	0.93[ASN][1000 genomes]
rs73114457	0.90[ASN][1000 genomes]
rs73114459	0.90[ASN][1000 genomes]
rs73114467	0.90[ASN][1000 genomes]
rs73114468	0.90[ASN][1000 genomes]
rs73114472	0.88[ASN][1000 genomes]
rs73116494	0.82[ASN][1000 genomes]
rs73116501	0.82[ASN][1000 genomes]
rs73131120	0.97[ASN][1000 genomes]
rs7314151	0.87[GIH][hapmap]
rs733629	0.90[CHB][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs746049	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7487948	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs754398	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs755221	0.90[ASN][1000 genomes]
rs7956166	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7961920	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs7962771	1.00[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs7969312	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7972615	0.90[CHB][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs840160	0.82[GIH][hapmap]
rs901068	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1040850	chr12:57055011-57679209	Strong transcription Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	181 gene(s)	inside rSNPs	diseases
2	nsv428590	chr12:57329214-57527358	Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
3	nsv899109	chr12:57331741-57381259	Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases
4	nsv559021	chr12:57338716-57381259	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases
5	nsv832428	chr12:57340609-57535694	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7136770	RDH16	cis	cerebellum	SCAN
rs7136770	GLI1	cis	parietal	SCAN
rs7136770	ZBTB39	cis	parietal	SCAN

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:57361800-57389000	Weak transcription	Aorta	Aorta
2	chr12:57372000-57384800	Weak transcription	Gastric	stomach
3	chr12:57372200-57384800	Weak transcription	Primary T cells from cord blood	blood
4	chr12:57373200-57388600	Weak transcription	Fetal Brain Female	brain
5	chr12:57373200-57388800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr12:57375200-57381600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr12:57377000-57395200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr12:57379200-57382400	Enhancers	NHEK	skin
9	chr12:57379600-57381400	Enhancers	HMEC	breast
10	chr12:57379600-57381400	Enhancers	K562	blood
11	chr12:57379600-57382400	Enhancers	Fetal Thymus	thymus
12	chr12:57379800-57381400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr12:57379800-57381400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr12:57379800-57381400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr12:57379800-57381400	Enhancers	Placenta Amnion	Placenta Amnion
16	chr12:57379800-57381600	Enhancers	Breast Myoepithelial Primary Cells	Breast
17	chr12:57380000-57381400	Enhancers	Esophagus	oesophagus
18	chr12:57380000-57381600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr12:57380000-57381800	Weak transcription	HSMMtube	muscle
20	chr12:57380000-57382200	Enhancers	Liver	Liver
21	chr12:57380000-57391400	Weak transcription	Fetal Intestine Large	intestine
22	chr12:57380200-57381600	Weak transcription	Hela-S3	cervix
23	chr12:57380200-57381800	Enhancers	Lung	lung
24	chr12:57380200-57385400	Weak transcription	HepG2	liver
25	chr12:57380400-57382600	Weak transcription	A549	lung
26	chr12:57380800-57383000	Enhancers	Primary hematopoietic stem cells	blood
27	chr12:57380800-57383200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
28	chr12:57380800-57385000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr12:57381000-57381400	Enhancers	Brain Substantia Nigra	brain
30	chr12:57381000-57381400	Enhancers	Rectal Smooth Muscle	rectum
31	chr12:57381000-57381400	Enhancers	Thymus	Thymus
32	chr12:57381000-57381800	Enhancers	Primary T cells fromperipheralblood	blood
33	chr12:57381000-57381800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
34	chr12:57381000-57381800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr12:57381000-57381800	Enhancers	Pancreas	Pancrea
36	chr12:57381000-57381800	Enhancers	Spleen	Spleen
37	chr12:57381000-57381800	Enhancers	Dnd41	blood
38	chr12:57381000-57382000	Enhancers	Brain Inferior Temporal Lobe	brain
39	chr12:57381000-57382200	Enhancers	Colon Smooth Muscle	Colon
40	chr12:57381000-57382200	Enhancers	Skeletal Muscle Male	skeletal muscle
41	chr12:57381000-57382400	Enhancers	Right Ventricle	heart
42	chr12:57381000-57382400	Enhancers	Skeletal Muscle Female	skeletal muscle
43	chr12:57381000-57382600	Enhancers	ES-I3 Cell Line	embryonic stem cell
44	chr12:57381000-57382600	Enhancers	Brain Hippocampus Middle	brain
45	chr12:57381000-57382600	Enhancers	Fetal Muscle Leg	muscle
46	chr12:57381000-57383200	Enhancers	Primary hematopoietic stem cells short term culture	blood
47	chr12:57381200-57381400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr12:57381200-57381400	Enhancers	Primary B cells from cord blood	blood
49	chr12:57381200-57381400	Enhancers	Primary T helper cells PMA-I stimulated	--
50	chr12:57381200-57381400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain

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