Variant report

Variant	rs921973
Chromosome Location	chr6:70406462-70406463
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:70401464..70403488-chr6:70405227..70406858,2	K562	blood:

Extended variants
information (count: 64 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs1031631	0.93[LWK][hapmap];0.92[MKK][hapmap];0.84[YRI][hapmap];0.87[AFR][1000 genomes]
rs11970363	0.93[LWK][hapmap];0.92[MKK][hapmap];0.85[YRI][hapmap]
rs12055543	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12665798	0.93[LWK][hapmap];0.92[MKK][hapmap];0.82[AFR][1000 genomes]
rs1457499	0.85[YRI][hapmap];0.91[AFR][1000 genomes]
rs1457500	0.91[AFR][1000 genomes]
rs1542413	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1563608	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1563610	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs1840940	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1840942	0.89[ASN][1000 genomes]
rs1902650	0.87[AFR][1000 genomes]
rs1993482	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2061310	0.89[LWK][hapmap];0.92[MKK][hapmap];0.90[AFR][1000 genomes]
rs2168712	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2345564	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.80[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs2445957	0.81[YRI][hapmap];0.84[AFR][1000 genomes]
rs2445958	0.91[LWK][hapmap];0.92[MKK][hapmap];0.84[AFR][1000 genomes]
rs2445959	0.84[AFR][1000 genomes]
rs2445960	0.84[AFR][1000 genomes]
rs2445962	0.83[AFR][1000 genomes]
rs2445964	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2445973	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2445974	0.89[ASN][1000 genomes]
rs2445976	0.95[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2494776	1.00[ASN][1000 genomes]
rs2502543	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2502564	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2502597	0.84[CEU][hapmap];0.80[YRI][hapmap];0.84[AFR][1000 genomes]
rs3778241	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs3799112	0.93[LWK][hapmap];0.92[MKK][hapmap];0.85[YRI][hapmap];0.90[AFR][1000 genomes]
rs3799113	0.85[YRI][hapmap];0.86[AFR][1000 genomes]
rs3806960	0.93[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.92[YRI][hapmap];0.88[ASN][1000 genomes]
rs5027848	0.80[AFR][1000 genomes]
rs6455337	0.81[AFR][1000 genomes]
rs6455340	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6455342	0.81[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs6455344	0.87[EUR][1000 genomes]
rs6905645	0.86[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[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];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6935590	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7742015	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];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7747908	0.92[ASN][1000 genomes]
rs7749324	0.85[YRI][hapmap]
rs7749509	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7758405	0.93[LWK][hapmap];0.92[MKK][hapmap];0.85[YRI][hapmap];0.86[AFR][1000 genomes]
rs7763213	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7771508	0.83[AFR][1000 genomes]
rs7774371	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9185	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];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9294848	0.81[AFR][1000 genomes]
rs930886	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9342766	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9342768	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9346340	0.86[AFR][1000 genomes]
rs9346341	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9346342	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9354876	0.81[AFR][1000 genomes]
rs9354884	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9360400	0.81[AFR][1000 genomes]
rs9364046	0.81[AFR][1000 genomes]
rs9364050	0.84[AFR][1000 genomes]
rs960144	0.84[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv886140	chr6:70354682-70728202	Strong transcription Enhancers Genic enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
2	nsv830682	chr6:70397851-70592883	Weak transcription Strong transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs921973	SMAP1	cis	parietal	SCAN

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:70378800-70407400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr6:70378800-70409600	Weak transcription	Brain Substantia Nigra	brain
3	chr6:70378800-70416800	Weak transcription	Fetal Kidney	kidney
4	chr6:70378800-70430800	Weak transcription	Fetal Stomach	stomach
5	chr6:70378800-70430800	Weak transcription	Spleen	Spleen
6	chr6:70378800-70435200	Weak transcription	Psoas Muscle	Psoas
7	chr6:70379000-70428400	Weak transcription	Ovary	ovary
8	chr6:70379000-70435400	Weak transcription	Fetal Brain Male	brain
9	chr6:70379600-70431000	Weak transcription	Rectal Smooth Muscle	rectum
10	chr6:70380200-70407600	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr6:70380400-70430600	Weak transcription	Fetal Intestine Small	intestine
12	chr6:70380600-70455600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr6:70380800-70467800	Weak transcription	K562	blood
14	chr6:70382200-70435400	Weak transcription	Brain Angular Gyrus	brain
15	chr6:70382400-70430200	Weak transcription	Small Intestine	intestine
16	chr6:70383800-70407800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
17	chr6:70383800-70431000	Weak transcription	Lung	lung
18	chr6:70384000-70415800	Weak transcription	Fetal Lung	lung
19	chr6:70384200-70428400	Weak transcription	Aorta	Aorta
20	chr6:70384200-70431000	Weak transcription	Fetal Muscle Leg	muscle
21	chr6:70384400-70407200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr6:70384600-70407800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
23	chr6:70384600-70407800	Weak transcription	Stomach Smooth Muscle	stomach
24	chr6:70384600-70409800	Weak transcription	Brain Hippocampus Middle	brain
25	chr6:70384600-70417400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr6:70385000-70407600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr6:70385000-70421600	Weak transcription	Fetal Intestine Large	intestine
28	chr6:70386400-70408000	Weak transcription	Placenta	Placenta
29	chr6:70387000-70407800	Weak transcription	Dnd41	blood
30	chr6:70387200-70407400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr6:70387200-70407800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr6:70387400-70407400	Weak transcription	Fetal Thymus	thymus
33	chr6:70387600-70407800	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr6:70387600-70415600	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr6:70388000-70423400	Weak transcription	Left Ventricle	heart
36	chr6:70395400-70407200	Weak transcription	Primary T cells fromperipheralblood	blood
37	chr6:70396200-70412200	Strong transcription	Primary B cells from peripheral blood	blood
38	chr6:70397200-70410200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
39	chr6:70397200-70415600	Weak transcription	Primary T cells from cord blood	blood
40	chr6:70397800-70439000	Weak transcription	Fetal Heart	heart
41	chr6:70398000-70423000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
42	chr6:70399400-70407400	Weak transcription	Skeletal Muscle Female	skeletal muscle
43	chr6:70400800-70430800	Weak transcription	Pancreas	Pancrea
44	chr6:70402000-70412000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
45	chr6:70402000-70430800	Weak transcription	Esophagus	oesophagus
46	chr6:70402200-70435200	Weak transcription	Brain Anterior Caudate	brain
47	chr6:70402800-70430800	Weak transcription	Fetal Muscle Trunk	muscle
48	chr6:70403000-70429800	Weak transcription	NHDF-Ad	bronchial
49	chr6:70403200-70415400	Weak transcription	HSMM	muscle
50	chr6:70403400-70432200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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