Variant report

Variant	rs9398214
Chromosome Location	chr6:110039740-110039741
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 95 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:90)

rs_ID	r²[population]
rs10659	1.00[CEU][hapmap]
rs10872052	0.82[CHB][hapmap]
rs11153200	0.82[CHB][hapmap]
rs11968485	0.82[CHB][hapmap]
rs12215867	0.82[CHB][hapmap]
rs12524352	0.81[CHB][hapmap]
rs1321207	0.90[LWK][hapmap]
rs1321327	0.82[CHB][hapmap]
rs13437149	1.00[CEU][hapmap];0.92[CHB][hapmap];0.94[JPT][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1406957	0.82[CHB][hapmap]
rs1474959	0.82[CHB][hapmap]
rs1570013	0.82[CHB][hapmap]
rs17070874	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17070970	1.00[CEU][hapmap]
rs17070972	1.00[CEU][hapmap]
rs17070984	1.00[CEU][hapmap]
rs2016207	0.82[CHB][hapmap]
rs2076929	1.00[CEU][hapmap];0.90[CHB][hapmap];0.94[YRI][hapmap];0.91[AMR][1000 genomes]
rs2145144	0.82[CHB][hapmap]
rs2295835	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2295836	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.88[LWK][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3823235	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4512266	1.00[CEU][hapmap]
rs4523125	0.82[CHB][hapmap]
rs4946992	0.82[CHB][hapmap]
rs6568580	0.82[CHB][hapmap]
rs6568587	1.00[CEU][hapmap];0.91[CHB][hapmap];0.90[YRI][hapmap];0.82[AMR][1000 genomes]
rs6568595	0.82[CHB][hapmap]
rs6900091	0.91[AMR][1000 genomes]
rs6916239	0.88[CHB][hapmap]
rs6917383	1.00[CEU][hapmap];0.91[CHB][hapmap];0.90[YRI][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs6924269	0.82[CHB][hapmap]
rs6925005	0.92[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.83[GIH][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.82[AMR][1000 genomes]
rs6933729	1.00[CEU][hapmap]
rs73535341	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7356790	0.92[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.83[GIH][hapmap];0.97[LWK][hapmap];0.85[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.91[AMR][1000 genomes]
rs7450970	0.82[CHB][hapmap]
rs7453835	0.82[CHB][hapmap]
rs7740192	0.91[AMR][1000 genomes]
rs7742066	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7743159	0.91[AMR][1000 genomes]
rs7744512	1.00[CEU][hapmap]
rs7744981	0.82[CHB][hapmap]
rs7745469	0.82[CHB][hapmap]
rs7749605	0.90[CHB][hapmap];0.91[AMR][1000 genomes]
rs7749910	0.82[CHB][hapmap]
rs7761008	0.82[CHB][hapmap]
rs7765916	1.00[CEU][hapmap];0.91[CHB][hapmap];0.89[YRI][hapmap];0.91[AMR][1000 genomes]
rs7767805	0.84[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];0.83[GIH][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes]
rs7775092	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs829816	0.82[CHB][hapmap]
rs927127	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs9320304	0.82[CHB][hapmap]
rs9372222	0.82[CHB][hapmap]
rs9372225	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9372226	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.88[LWK][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9374095	0.82[CHB][hapmap]
rs9374097	0.82[CHB][hapmap]
rs9374108	0.82[CHB][hapmap]
rs9374110	0.88[CHB][hapmap]
rs9374114	0.82[CHB][hapmap]
rs9374117	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9374121	0.92[CHB][hapmap];0.88[CHD][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs9386813	0.82[CHB][hapmap]
rs9386818	0.82[CHB][hapmap]
rs9386823	0.81[CHB][hapmap]
rs9386824	0.82[CHB][hapmap]
rs9386826	0.89[CHB][hapmap]
rs9386833	0.91[AMR][1000 genomes]
rs9386835	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9386842	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9398215	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9400310	0.82[CHB][hapmap]
rs9400312	0.81[CHB][hapmap]
rs9400316	0.82[CHB][hapmap]
rs9480973	0.81[CHB][hapmap]
rs9480984	0.82[CHB][hapmap]
rs9480990	0.81[AMR][1000 genomes]
rs9480991	0.82[CHB][hapmap]
rs9481003	0.82[CEU][hapmap];0.85[TSI][hapmap]
rs9487171	0.82[CHB][hapmap]
rs9487172	0.82[CHB][hapmap]
rs9487175	0.82[CHB][hapmap]
rs9487176	0.82[CHB][hapmap]
rs9487180	0.82[CHB][hapmap]
rs9487186	0.91[AMR][1000 genomes]
rs9487193	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9487203	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs971432	0.82[CHB][hapmap]
rs9986507	0.82[CHB][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	nsv933105	chr6:109933270-110064342	ZNF genes & repeats Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
3	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
4	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
5	nsv604485	chr6:109959269-110054486	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:110013000-110057000	Weak transcription	Left Ventricle	heart
2	chr6:110013000-110114400	Weak transcription	Right Ventricle	heart
3	chr6:110013200-110057000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr6:110013200-110057000	Weak transcription	Aorta	Aorta
5	chr6:110013600-110056000	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr6:110013600-110056800	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr6:110024200-110056400	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr6:110025000-110057000	Weak transcription	Fetal Thymus	thymus
9	chr6:110027000-110040400	Weak transcription	Primary T helper cells PMA-I stimulated	--
10	chr6:110027000-110052400	Weak transcription	Liver	Liver
11	chr6:110027000-110056400	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr6:110028000-110044000	Weak transcription	Brain Angular Gyrus	brain
13	chr6:110028000-110071200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr6:110028200-110057200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
15	chr6:110028200-110080800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr6:110033200-110041000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr6:110034400-110041600	Weak transcription	Brain Substantia Nigra	brain
18	chr6:110034400-110042200	Weak transcription	NHLF	lung
19	chr6:110034400-110044400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr6:110034400-110060800	Weak transcription	Fetal Stomach	stomach
21	chr6:110034600-110041600	Weak transcription	Brain Cingulate Gyrus	brain
22	chr6:110034600-110041800	Weak transcription	NHDF-Ad	bronchial
23	chr6:110034600-110046600	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr6:110034600-110056400	Weak transcription	Fetal Brain Female	brain
25	chr6:110034600-110057000	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr6:110034800-110040200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr6:110034800-110042000	Weak transcription	Lung	lung
28	chr6:110034800-110042400	Weak transcription	Brain Anterior Caudate	brain
29	chr6:110034800-110059000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr6:110035000-110044000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr6:110035000-110071400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr6:110035000-110084000	Weak transcription	GM12878-XiMat	blood
33	chr6:110035200-110040400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
34	chr6:110035200-110056200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr6:110035200-110065000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr6:110035200-110094200	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr6:110035400-110040800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr6:110035400-110057800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr6:110035400-110083000	Weak transcription	Brain Germinal Matrix	brain
40	chr6:110035600-110040200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr6:110035600-110040200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr6:110035600-110040600	Weak transcription	Gastric	stomach
43	chr6:110035600-110042000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr6:110035600-110044000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr6:110035600-110045000	Weak transcription	Fetal Muscle Leg	muscle
46	chr6:110035600-110056400	Weak transcription	Ovary	ovary
47	chr6:110035600-110057000	Weak transcription	Pancreas	Pancrea
48	chr6:110035600-110089000	Weak transcription	Spleen	Spleen
49	chr6:110035800-110057000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr6:110035800-110065000	Weak transcription	HSMM	muscle

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