Variant report

Variant	rs6941360
Chromosome Location	chr6:110068786-110068787
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 53 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs11751112	0.83[TSI][hapmap]
rs11968485	0.88[TSI][hapmap]
rs12171561	0.98[ASN][1000 genomes]
rs12215867	0.88[TSI][hapmap]
rs13437149	0.81[JPT][hapmap]
rs1406957	0.88[TSI][hapmap]
rs1474959	0.88[TSI][hapmap]
rs17612996	0.82[CEU][hapmap]
rs2145144	0.88[TSI][hapmap]
rs2224550	0.86[MKK][hapmap]
rs2295836	0.81[JPT][hapmap]
rs2357128	0.82[CEU][hapmap];0.95[CHB][hapmap];0.91[GIH][hapmap];0.85[MEX][hapmap];0.90[TSI][hapmap]
rs2357226	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3823235	0.80[JPT][hapmap]
rs4523125	0.88[TSI][hapmap]
rs4946992	0.88[TSI][hapmap]
rs6568598	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6568600	0.82[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap];0.90[MEX][hapmap];0.96[MKK][hapmap];0.90[TSI][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6568602	0.87[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.93[LWK][hapmap];0.95[MEX][hapmap];0.99[MKK][hapmap];0.93[TSI][hapmap];0.87[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6568603	0.87[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.93[LWK][hapmap];0.95[MEX][hapmap];0.99[MKK][hapmap];0.93[TSI][hapmap];0.87[YRI][hapmap];0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7450970	0.88[TSI][hapmap]
rs7744981	0.80[MEX][hapmap];0.88[TSI][hapmap]
rs7745469	0.88[TSI][hapmap]
rs7749910	0.88[TSI][hapmap]
rs7758697	0.98[ASN][1000 genomes]
rs829813	0.82[CEU][hapmap];0.94[CHB][hapmap];0.91[GIH][hapmap];0.85[MEX][hapmap];0.87[TSI][hapmap]
rs829814	0.82[CEU][hapmap];0.95[CHB][hapmap]
rs829816	0.88[TSI][hapmap]
rs9372226	0.81[JPT][hapmap]
rs9374097	0.88[TSI][hapmap]
rs9374110	0.84[CEU][hapmap]
rs9374114	0.81[CEU][hapmap]
rs9374121	0.96[CEU][hapmap];0.82[GIH][hapmap];0.81[JPT][hapmap];0.81[MEX][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9384717	0.82[CEU][hapmap];0.95[CHB][hapmap];0.91[GIH][hapmap];0.85[MEX][hapmap];0.90[TSI][hapmap]
rs9386813	0.88[TSI][hapmap]
rs9386824	0.88[TSI][hapmap]
rs9386826	0.91[CEU][hapmap]
rs9386839	0.91[ASN][1000 genomes]
rs9400310	0.87[TSI][hapmap]
rs9400316	0.88[TSI][hapmap]
rs9400320	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.95[MEX][hapmap];0.96[MKK][hapmap];0.97[TSI][hapmap];0.92[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9480984	0.88[TSI][hapmap]
rs9480991	0.88[TSI][hapmap]
rs9481003	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs9487172	0.88[TSI][hapmap]
rs9487176	0.88[TSI][hapmap]
rs9487202	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9986507	0.88[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	nsv949475	chr6:109907936-110160501	Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv817322	chr6:109933272-110070574	Strong transcription Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
3	nsv830769	chr6:109944334-110078120	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
4	nsv5436	chr6:110052812-110097662	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	nsv886533	chr6:110067773-110126393	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6941360	SMPD2	cis	Whole Blood	GTEx
rs6941360	FLJ42177	cis	multi-tissue	Pritchard
rs6941360	SMPD2	cis	cerebellum	SCAN

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:110013000-110114400	Weak transcription	Right Ventricle	heart
2	chr6:110028000-110071200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr6:110028200-110080800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr6:110035000-110071400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr6:110035000-110084000	Weak transcription	GM12878-XiMat	blood
6	chr6:110035200-110094200	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr6:110035400-110083000	Weak transcription	Brain Germinal Matrix	brain
8	chr6:110035600-110089000	Weak transcription	Spleen	Spleen
9	chr6:110036800-110115600	Weak transcription	Colonic Mucosa	Colon
10	chr6:110039000-110081000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr6:110041400-110081000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr6:110042200-110088800	Weak transcription	Fetal Intestine Small	intestine
13	chr6:110042400-110089000	Weak transcription	Brain Cingulate Gyrus	brain
14	chr6:110044200-110115400	Weak transcription	Brain Angular Gyrus	brain
15	chr6:110047200-110084000	Weak transcription	Small Intestine	intestine
16	chr6:110047600-110068800	Weak transcription	Dnd41	blood
17	chr6:110048600-110089800	Weak transcription	Fetal Kidney	kidney
18	chr6:110050400-110078400	Weak transcription	Fetal Brain Male	brain
19	chr6:110057200-110089000	Weak transcription	Fetal Brain Female	brain
20	chr6:110057400-110089000	Weak transcription	Esophagus	oesophagus
21	chr6:110057600-110086200	Weak transcription	Brain Anterior Caudate	brain
22	chr6:110058200-110087200	Weak transcription	Rectal Smooth Muscle	rectum
23	chr6:110058200-110089000	Weak transcription	Lung	lung
24	chr6:110058400-110085000	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr6:110058400-110089600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr6:110058800-110112400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
27	chr6:110059200-110069400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr6:110059200-110124000	Weak transcription	Colon Smooth Muscle	Colon
29	chr6:110060000-110087800	Weak transcription	Fetal Thymus	thymus
30	chr6:110061200-110089200	Weak transcription	Pancreas	Pancrea
31	chr6:110062600-110089200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
32	chr6:110062800-110087400	Weak transcription	HUES64 Cell Line	embryonic stem cell
33	chr6:110062800-110088000	Weak transcription	Rectal Mucosa Donor 31	rectum
34	chr6:110063000-110078000	Weak transcription	Primary hematopoietic stem cells	blood
35	chr6:110065200-110084000	Weak transcription	Left Ventricle	heart
36	chr6:110065200-110089000	Weak transcription	Skeletal Muscle Male	skeletal muscle
37	chr6:110065200-110111200	Weak transcription	HUES48 Cell Line	embryonic stem cell
38	chr6:110065400-110094200	Weak transcription	Brain Substantia Nigra	brain
39	chr6:110065600-110069000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr6:110065600-110069200	Weak transcription	Aorta	Aorta
41	chr6:110065600-110069600	Weak transcription	Liver	Liver
42	chr6:110065600-110070000	Weak transcription	Fetal Muscle Trunk	muscle
43	chr6:110065600-110070400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr6:110065600-110073000	Weak transcription	Stomach Smooth Muscle	stomach
45	chr6:110065600-110074200	Weak transcription	Fetal Intestine Large	intestine
46	chr6:110065600-110074400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr6:110065600-110077800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr6:110065600-110080800	Weak transcription	Sigmoid Colon	Sigmoid Colon
49	chr6:110065600-110084000	Weak transcription	Placenta	Placenta
50	chr6:110065600-110087200	Weak transcription	HSMMtube	muscle

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