Variant report

Variant	rs2950390
Chromosome Location	chr12:57055291-57055292
allele	C/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:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:57054749..57057054-chr12:57058615..57061624,4	K562	blood:
2	chr12:57051978..57057362-chr12:57059430..57061597,6	K562	blood:
3	chr12:57029048..57031672-chr12:57053397..57055305,2	K562	blood:
4	chr12:57053497..57055656-chr12:57080876..57083065,2	MCF-7	breast:
5	chr12:57036892..57041043-chr12:57050765..57055659,6	MCF-7	breast:
6	chr12:57053284..57055911-chr12:57082138..57083741,2	MCF-7	breast:
7	chr12:57054945..57056798-chr12:57071104..57072974,2	K562	blood:
8	chr12:57036157..57038877-chr12:57054362..57057150,2	K562	blood:
9	chr12:56916195..56918397-chr12:57055172..57057323,2	K562	blood:
10	chr12:57026992..57029615-chr12:57053827..57055942,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000110955	Chromatin interaction
ENSG00000207031	Chromatin interaction
ENSG00000110958	Chromatin interaction
ENSG00000076108	Chromatin interaction

Extended variants
information (count: 75 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs1020848	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1026565	0.90[CEU][hapmap];0.87[CHB][hapmap];0.86[TSI][hapmap]
rs10450	0.80[CHB][hapmap];0.95[JPT][hapmap]
rs10747769	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10783794	0.81[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs10876913	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10876914	1.00[ASN][1000 genomes]
rs10876915	1.00[ASN][1000 genomes]
rs10876916	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1107479	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11171914	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11171916	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11171917	1.00[ASN][1000 genomes]
rs11171951	0.89[CEU][hapmap];0.93[CHB][hapmap];0.81[JPT][hapmap];0.82[TSI][hapmap]
rs11835120	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11837319	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12229457	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1465081	1.00[ASN][1000 genomes]
rs1466382	0.93[CHB][hapmap];0.81[CHD][hapmap]
rs1563896	0.95[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1563897	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1962963	0.88[ASN][1000 genomes]
rs1979325	0.93[CHB][hapmap]
rs2035081	0.90[CEU][hapmap];0.87[CHB][hapmap];0.81[CHD][hapmap];0.84[TSI][hapmap]
rs2255074	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2290893	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2290894	0.90[CEU][hapmap];0.93[CHB][hapmap]
rs2926740	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2926741	0.90[CEU][hapmap];0.93[CHB][hapmap]
rs2926743	0.93[CHB][hapmap];0.81[CHD][hapmap]
rs2950387	0.87[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.93[ASN][1000 genomes]
rs2950388	1.00[ASN][1000 genomes]
rs2950389	0.90[JPT][hapmap]
rs2950393	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2950394	1.00[ASN][1000 genomes]
rs2958123	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2958124	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2958127	0.90[CEU][hapmap];0.93[CHB][hapmap];0.81[CHD][hapmap];0.84[TSI][hapmap]
rs2958130	0.90[CEU][hapmap];0.93[CHB][hapmap];0.81[CHD][hapmap];0.84[TSI][hapmap]
rs2958145	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2958146	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2958148	0.89[CEU][hapmap]
rs2958149	0.87[CHB][hapmap]
rs2958153	1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.91[ASN][1000 genomes]
rs2958154	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];1.00[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]
rs2958155	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3214051	0.90[CEU][hapmap];0.93[CHB][hapmap];0.81[CHD][hapmap];0.84[TSI][hapmap]
rs36012661	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4759028	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4759254	0.80[CEU][hapmap];0.91[CHB][hapmap];0.94[JPT][hapmap]
rs67046307	1.00[ASN][1000 genomes]
rs7295862	1.00[CEU][hapmap]
rs7297289	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7303216	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7313074	0.93[CHB][hapmap];0.81[CHD][hapmap];0.83[MEX][hapmap]
rs7315472	1.00[ASN][1000 genomes]
rs73337030	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7967600	0.90[CEU][hapmap];0.93[CHB][hapmap];0.81[CHD][hapmap]
rs7972420	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7973157	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7975783	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7978685	0.93[CHB][hapmap];0.81[CHD][hapmap];0.83[MEX][hapmap]
rs7980317	0.90[CEU][hapmap];0.93[CHB][hapmap];0.81[CHD][hapmap]
rs7980378	0.94[ASN][1000 genomes]
rs7980835	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs898609	0.90[CEU][hapmap];0.93[CHB][hapmap]
rs898611	0.90[CEU][hapmap];0.93[CHB][hapmap];0.81[CHD][hapmap]
rs9368	0.81[CHB][hapmap]
rs941207	0.93[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs941209	0.84[JPT][hapmap]
rs9634246	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9634247	0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9634277	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9989034	0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 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

Variant related diseases (count:1)

Disease	PMID	Source
Mean platelet volume	22139419	GWAS catalog

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs2950390	PRIM1	cis	parietal	SCAN
rs2950390	GPR182	cis	parietal	SCAN
rs2950390	KRT1	cis	cerebellum	SCAN
rs2950390	OR10A7	cis	parietal	SCAN
rs2950390	RBMS2	cis	multi-tissue	Pritchard
rs2950390	ERBB3	cis	parietal	SCAN
rs2950390	CELA1	cis	cerebellum	SCAN
rs2950390	PRIM1	cis	cerebellum	SCAN
rs2950390	LETMD1	cis	cerebellum	SCAN
rs2950390	HSD17B6	cis	cerebellum	SCAN
rs2950390	HOXC6	cis	cerebellum	SCAN
rs2950390	SPRYD3	cis	parietal	SCAN
rs2950390	IL23A	cis	cerebellum	SCAN

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:57039800-57055800	Weak transcription	Gastric	stomach
2	chr12:57039800-57059200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr12:57040400-57056200	Weak transcription	Fetal Muscle Trunk	muscle
4	chr12:57040400-57059200	Weak transcription	Aorta	Aorta
5	chr12:57040400-57059400	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr12:57040400-57069400	Weak transcription	Right Atrium	heart
7	chr12:57040600-57056400	Weak transcription	Brain Substantia Nigra	brain
8	chr12:57040600-57056400	Weak transcription	Colonic Mucosa	Colon
9	chr12:57040600-57056400	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr12:57040600-57056800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr12:57040600-57058200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr12:57040600-57058200	Weak transcription	Colon Smooth Muscle	Colon
13	chr12:57040600-57058800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr12:57046200-57059400	Weak transcription	Lung	lung
15	chr12:57047000-57055600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr12:57048000-57055600	Weak transcription	Stomach Smooth Muscle	stomach
17	chr12:57048800-57056800	Weak transcription	Dnd41	blood
18	chr12:57049400-57056200	Weak transcription	Fetal Muscle Leg	muscle
19	chr12:57049800-57056200	Weak transcription	Left Ventricle	heart
20	chr12:57050200-57055800	Weak transcription	Fetal Stomach	stomach
21	chr12:57051400-57056600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr12:57051400-57056800	Weak transcription	HSMM	muscle
23	chr12:57051400-57057800	Weak transcription	Brain Cingulate Gyrus	brain
24	chr12:57051400-57058000	Weak transcription	Brain Hippocampus Middle	brain
25	chr12:57051400-57058400	Weak transcription	Brain Angular Gyrus	brain
26	chr12:57051400-57058600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr12:57051600-57056400	Weak transcription	Primary T helper cells PMA-I stimulated	--
28	chr12:57051800-57055400	Weak transcription	A549	lung
29	chr12:57052000-57056200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
30	chr12:57052000-57059200	Weak transcription	Spleen	Spleen
31	chr12:57052200-57055600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr12:57052200-57055600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr12:57052400-57055600	Weak transcription	Adipose Nuclei	Adipose
34	chr12:57052400-57059200	Weak transcription	NHLF	lung
35	chr12:57052400-57078200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
36	chr12:57052600-57056200	Weak transcription	Duodenum Mucosa	Duodenum
37	chr12:57052600-57059800	Weak transcription	Primary hematopoietic stem cells	blood
38	chr12:57053000-57056200	Weak transcription	Skeletal Muscle Female	skeletal muscle
39	chr12:57053000-57060200	Weak transcription	Right Ventricle	heart
40	chr12:57053200-57055400	Weak transcription	Fetal Intestine Small	intestine
41	chr12:57053200-57055600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr12:57053200-57055800	Weak transcription	Rectal Mucosa Donor 29	rectum
43	chr12:57053200-57056600	Weak transcription	GM12878-XiMat	blood
44	chr12:57053200-57057600	Weak transcription	Primary B cells from peripheral blood	blood
45	chr12:57053400-57055400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr12:57053400-57055400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr12:57053400-57055800	Weak transcription	Primary monocytes fromperipheralblood	blood
48	chr12:57053400-57055800	Weak transcription	Primary T cells from cord blood	blood
49	chr12:57053400-57056000	Weak transcription	Cortex derived primary cultured neurospheres	brain
50	chr12:57053400-57056600	Weak transcription	NH-A	brain

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