Variant report

Variant	rs12192420
Chromosome Location	chr6:119565900-119565901
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:119549395..119552818-chr6:119562345..119566202,3	K562	blood:
2	chr6:119558682..119563599-chr6:119563682..119567581,7	K562	blood:
3	chr6:119558122..119561935-chr6:119561959..119566839,6	K562	blood:

Extended variants
information (count: 94 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs1022869	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1022870	1.00[ASN][1000 genomes]
rs1028327	0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1028328	0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10456921	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10457352	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10457353	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10457355	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs10485001	0.96[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.82[MEX][hapmap];0.86[MKK][hapmap];0.95[TSI][hapmap];0.84[YRI][hapmap];0.80[AFR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10872173	0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10872177	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11153796	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11153797	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11153800	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11153803	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11153805	1.00[CEU][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11153808	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11153809	0.82[YRI][hapmap]
rs11153810	0.80[AFR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11153811	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11153812	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11751945	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11755967	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11759899	0.82[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.82[MEX][hapmap];0.83[MKK][hapmap];0.95[TSI][hapmap];0.84[YRI][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11961647	1.00[ASN][1000 genomes]
rs11962938	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12198423	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12198667	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12200554	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12205260	0.80[AFR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12205826	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12206472	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs12207595	0.90[EUR][1000 genomes]
rs12210002	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12524617	0.93[ASN][1000 genomes]
rs1295388	0.93[ASN][1000 genomes]
rs17514051	0.89[EUR][1000 genomes]
rs2036257	1.00[CHB][hapmap]
rs2038769	0.81[CEU][hapmap]
rs2092218	0.93[ASN][1000 genomes]
rs2142886	0.83[EUR][1000 genomes]
rs35433313	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4607463	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55778105	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61094987	0.85[ASN][1000 genomes]
rs6569056	0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6569057	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6569065	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6569066	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6569072	0.87[CEU][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.93[ASN][1000 genomes]
rs6569073	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6903249	1.00[ASN][1000 genomes]
rs6909928	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6913626	1.00[ASN][1000 genomes]
rs6913654	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6915559	0.86[GIH][hapmap];0.85[TSI][hapmap];0.82[YRI][hapmap]
rs6915947	0.86[GIH][hapmap];0.85[TSI][hapmap];0.82[YRI][hapmap]
rs6915957	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6918913	1.00[CHB][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];0.82[YRI][hapmap];1.00[ASN][1000 genomes]
rs6920832	0.93[ASN][1000 genomes]
rs6932241	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6932292	0.93[ASN][1000 genomes]
rs6935126	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.93[ASN][1000 genomes]
rs715373	0.82[YRI][hapmap]
rs715374	0.82[YRI][hapmap]
rs72960631	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73529045	0.93[ASN][1000 genomes]
rs73529086	0.93[ASN][1000 genomes]
rs7740993	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7741003	0.86[GIH][hapmap];0.85[TSI][hapmap]
rs7743299	0.90[EUR][1000 genomes]
rs7743824	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7750041	1.00[ASN][1000 genomes]
rs7750901	0.81[CEU][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap]
rs7750941	0.81[CEU][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap]
rs7753315	0.86[GIH][hapmap];0.85[TSI][hapmap];0.82[YRI][hapmap]
rs7753492	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7754482	0.87[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7756391	0.80[ASN][1000 genomes]
rs7760582	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7763569	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7767198	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7770398	0.81[CEU][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap]
rs7770777	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs926859	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9481900	0.81[CEU][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap]
rs9489669	1.00[JPT][hapmap];0.81[YRI][hapmap]
rs9489681	0.82[YRI][hapmap]
rs9489686	0.85[TSI][hapmap]

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	nsv1025995	chr6:119407742-119709548	Enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	nsv886570	chr6:119450888-119600556	Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv1017507	chr6:119465981-119664949	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	esv3447598	chr6:119558591-120119384	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
5	esv3389526	chr6:119558598-120190087	ZNF genes & repeats Enhancers Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12192420	RSPH4A	cis	parietal	SCAN

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:119547400-119583000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr6:119558800-119566200	Weak transcription	Primary B cells from cord blood	blood
3	chr6:119558800-119566200	Weak transcription	Left Ventricle	heart
4	chr6:119558800-119566200	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr6:119558800-119567400	Weak transcription	Primary monocytes fromperipheralblood	blood
6	chr6:119558800-119567400	Weak transcription	Primary T cells from cord blood	blood
7	chr6:119558800-119567400	Weak transcription	Primary hematopoietic stem cells	blood
8	chr6:119558800-119568000	Weak transcription	Placenta	Placenta
9	chr6:119558800-119568200	Weak transcription	Primary B cells from peripheral blood	blood
10	chr6:119558800-119568600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
11	chr6:119558800-119569200	Weak transcription	Primary T cells fromperipheralblood	blood
12	chr6:119558800-119569600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr6:119558800-119571800	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr6:119558800-119572000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr6:119558800-119572200	Weak transcription	Right Ventricle	heart
16	chr6:119558800-119572800	Weak transcription	Primary neutrophils fromperipheralblood	blood
17	chr6:119558800-119573600	Weak transcription	Lung	lung
18	chr6:119558800-119575200	Weak transcription	Esophagus	oesophagus
19	chr6:119558800-119576400	Weak transcription	Primary T helper cells PMA-I stimulated	--
20	chr6:119558800-119576400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
21	chr6:119558800-119576400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
22	chr6:119558800-119576400	Weak transcription	Dnd41	blood
23	chr6:119558800-119576600	Weak transcription	Spleen	Spleen
24	chr6:119558800-119576800	Weak transcription	Primary T helper cells fromperipheralblood	blood
25	chr6:119558800-119577600	Weak transcription	Aorta	Aorta
26	chr6:119558800-119578200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
27	chr6:119558800-119578200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr6:119558800-119578400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr6:119558800-119578600	Weak transcription	Fetal Thymus	thymus
30	chr6:119558800-119582200	Weak transcription	Colonic Mucosa	Colon
31	chr6:119558800-119589800	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr6:119558800-119590200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr6:119558800-119590400	Weak transcription	GM12878-XiMat	blood
34	chr6:119558800-119602000	Weak transcription	Gastric	stomach
35	chr6:119562200-119579400	Weak transcription	NHEK	skin
36	chr6:119562600-119567200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr6:119562600-119567400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr6:119562600-119567400	Weak transcription	Brain Anterior Caudate	brain
39	chr6:119562600-119568400	Weak transcription	Rectal Mucosa Donor 31	rectum
40	chr6:119562600-119568600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr6:119562600-119580000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr6:119562600-119580000	Weak transcription	Small Intestine	intestine
43	chr6:119562800-119566400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr6:119562800-119567400	Weak transcription	Colon Smooth Muscle	Colon
45	chr6:119562800-119568600	Weak transcription	Duodenum Mucosa	Duodenum
46	chr6:119562800-119582200	Weak transcription	Pancreas	Pancrea
47	chr6:119562800-119583000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr6:119562800-119590200	Weak transcription	Fetal Stomach	stomach
49	chr6:119562800-119590800	Weak transcription	Fetal Muscle Leg	muscle
50	chr6:119563000-119568400	Weak transcription	Duodenum Smooth Muscle	Duodenum

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