Variant report

Variant	rs10506350
Chromosome Location	chr12:57381675-57381676
allele	C/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:18)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:18 , 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	chr12:57232006..57233900-chr12:57381486..57383011,2	K562	blood:
4	chr12:57233421..57234366-chr12:57381033..57382023,8	MCF-7	breast:
5	chr12:57326458..57328470-chr12:57381157..57384002,3	MCF-7	breast:
6	chr12:57233353..57235203-chr12:57380743..57382388,18	MCF-7	breast:
7	chr12:57151018..57151992-chr12:57381056..57381889,5	MCF-7	breast:
8	chr12:57156921..57157570-chr12:57381033..57381981,4	MCF-7	breast:
9	chr12:57349736..57351385-chr12:57380003..57382609,2	MCF-7	breast:
10	chr12:57347864..57350577-chr12:57381566..57383920,2	MCF-7	breast:
11	chr12:57151005..57151996-chr12:57381006..57381955,2	K562	blood:
12	chr12:57341090..57342031-chr12:57380872..57381968,6	MCF-7	breast:
13	chr12:57381152..57386440-chr12:57387295..57390805,5	K562	blood:
14	chr12:57116564..57119483-chr12:57379649..57381889,2	MCF-7	breast:
15	chr12:57341567..57342147-chr12:57381088..57381948,3	MCF-7	breast:
16	chr12:57232928..57235574-chr12:57379321..57382266,3	MCF-7	breast:
17	chr12:57380979..57383508-chr12:57478377..57480452,2	MCF-7	breast:
18	chr12:57233059..57234536-chr12:57380344..57382025,8	K562	blood:

No data

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

Extended variants
information (count: 123 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:120)

rs_ID	r²[population]
rs10400412	0.96[ASN][1000 genomes]
rs10400555	0.96[ASN][1000 genomes]
rs1044939	0.90[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs10506347	0.91[CEU][hapmap];0.93[GIH][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes]
rs10506351	0.90[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs1072669	0.83[GIH][hapmap]
rs1072670	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11172071	0.85[GIH][hapmap]
rs11832487	0.95[ASN][1000 genomes]
rs11834851	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11834856	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11836517	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12099695	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12810024	0.91[CEU][hapmap];0.90[CHB][hapmap];0.92[CHD][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12810837	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12812499	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12815538	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12818342	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12824682	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12827039	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12827286	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1552245	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs1601405	0.83[GIH][hapmap]
rs17119301	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17119327	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs17119330	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs17119344	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs17119352	0.91[ASN][1000 genomes]
rs17119386	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs17119388	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs17119390	0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs17119407	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs17119416	1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs17119418	1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs1825514	0.80[GIH][hapmap]
rs1843311	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1843312	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1843313	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1872436	0.85[GIH][hapmap]
rs2035545	0.86[JPT][hapmap]
rs2167306	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2270736	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2270737	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2270739	0.90[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2279373	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2279743	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2291855	0.90[CHB][hapmap];0.86[JPT][hapmap];0.96[ASN][1000 genomes]
rs2371717	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs28589663	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2888139	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3024974	0.92[CHD][hapmap]
rs34186462	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34253098	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34359134	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34762603	0.83[ASN][1000 genomes]
rs34969650	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35034299	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35243318	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35493121	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs3782329	0.90[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs3782330	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs3803018	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs3894415	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4016338	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs4039	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs4143085	0.90[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs56128678	0.91[ASN][1000 genomes]
rs56270558	0.91[ASN][1000 genomes]
rs56354404	0.91[ASN][1000 genomes]
rs57056392	0.93[ASN][1000 genomes]
rs57129030	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57351760	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57558853	0.96[ASN][1000 genomes]
rs58298943	0.99[ASN][1000 genomes]
rs58389529	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs60258120	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60273384	1.00[ASN][1000 genomes]
rs60380217	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61504157	0.93[ASN][1000 genomes]
rs67476535	1.00[ASN][1000 genomes]
rs67771054	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs67844278	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs68126184	0.99[ASN][1000 genomes]
rs697222	0.81[CHD][hapmap];0.87[GIH][hapmap];0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs7135297	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7136770	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]
rs71461303	0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72482268	1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7298475	1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs73114426	0.96[ASN][1000 genomes]
rs73114428	0.96[ASN][1000 genomes]
rs73114434	0.96[ASN][1000 genomes]
rs73114436	0.96[ASN][1000 genomes]
rs73114437	0.94[ASN][1000 genomes]
rs73114446	0.91[ASN][1000 genomes]
rs73114452	0.91[ASN][1000 genomes]
rs73114457	0.91[ASN][1000 genomes]
rs73114459	0.91[ASN][1000 genomes]
rs73114467	0.91[ASN][1000 genomes]
rs73114468	0.91[ASN][1000 genomes]
rs73114472	0.89[ASN][1000 genomes]
rs73116494	0.83[ASN][1000 genomes]
rs73116501	0.83[ASN][1000 genomes]
rs73118413	0.81[ASN][1000 genomes]
rs73131120	0.99[ASN][1000 genomes]
rs7314151	0.90[GIH][hapmap]
rs7314262	0.83[GIH][hapmap]
rs733629	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs746049	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7487948	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs754398	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs755221	0.91[ASN][1000 genomes]
rs7956166	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7961920	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs7962771	1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs7969312	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7972615	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs840160	0.85[GIH][hapmap]
rs901068	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs901069	0.82[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 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	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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10506350	ZBTB39	cis	parietal	SCAN
rs10506350	GLI1	cis	parietal	SCAN
rs10506350	RDH16	cis	cerebellum	SCAN
rs10506350	STAT6	cis	multi-tissue	Pritchard

Chromatin state (count:90 , 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	chr12:57377000-57395200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr12:57379200-57382400	Enhancers	NHEK	skin
8	chr12:57379600-57382400	Enhancers	Fetal Thymus	thymus
9	chr12:57380000-57381800	Weak transcription	HSMMtube	muscle
10	chr12:57380000-57382200	Enhancers	Liver	Liver
11	chr12:57380000-57391400	Weak transcription	Fetal Intestine Large	intestine
12	chr12:57380200-57381800	Enhancers	Lung	lung
13	chr12:57380200-57385400	Weak transcription	HepG2	liver
14	chr12:57380400-57382600	Weak transcription	A549	lung
15	chr12:57380800-57383000	Enhancers	Primary hematopoietic stem cells	blood
16	chr12:57380800-57383200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
17	chr12:57380800-57385000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr12:57381000-57381800	Enhancers	Primary T cells fromperipheralblood	blood
19	chr12:57381000-57381800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
20	chr12:57381000-57381800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr12:57381000-57381800	Enhancers	Pancreas	Pancrea
22	chr12:57381000-57381800	Enhancers	Spleen	Spleen
23	chr12:57381000-57381800	Enhancers	Dnd41	blood
24	chr12:57381000-57382000	Enhancers	Brain Inferior Temporal Lobe	brain
25	chr12:57381000-57382200	Enhancers	Colon Smooth Muscle	Colon
26	chr12:57381000-57382200	Enhancers	Skeletal Muscle Male	skeletal muscle
27	chr12:57381000-57382400	Enhancers	Right Ventricle	heart
28	chr12:57381000-57382400	Enhancers	Skeletal Muscle Female	skeletal muscle
29	chr12:57381000-57382600	Enhancers	ES-I3 Cell Line	embryonic stem cell
30	chr12:57381000-57382600	Enhancers	Brain Hippocampus Middle	brain
31	chr12:57381000-57382600	Enhancers	Fetal Muscle Leg	muscle
32	chr12:57381000-57383200	Enhancers	Primary hematopoietic stem cells short term culture	blood
33	chr12:57381200-57381800	Enhancers	HUES64 Cell Line	embryonic stem cell
34	chr12:57381200-57381800	Enhancers	Primary B cells from peripheral blood	blood
35	chr12:57381200-57381800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
36	chr12:57381200-57381800	Enhancers	Primary T helper naive cells from peripheral blood	blood
37	chr12:57381200-57381800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
38	chr12:57381200-57381800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
39	chr12:57381200-57381800	Enhancers	Primary T helper cells fromperipheralblood	blood
40	chr12:57381200-57381800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
41	chr12:57381200-57381800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr12:57381200-57381800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
43	chr12:57381200-57381800	Enhancers	Brain Angular Gyrus	brain
44	chr12:57381200-57381800	Enhancers	Brain Anterior Caudate	brain
45	chr12:57381200-57381800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
46	chr12:57381200-57382000	Enhancers	HUES48 Cell Line	embryonic stem cell
47	chr12:57381200-57382000	Enhancers	Primary T killer memory cells from peripheral blood	blood
48	chr12:57381200-57382200	Enhancers	Ovary	ovary
49	chr12:57381200-57382400	Enhancers	Primary neutrophils fromperipheralblood	blood
50	chr12:57381200-57382600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung

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