Variant report

Variant	rs10971667
Chromosome Location	chr9:3382962-3382963
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 70 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10117357	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs10117431	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs10124292	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs10124295	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs10511447	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs10814019	0.93[ASN][1000 genomes]
rs10814038	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs10814039	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10814097	0.80[CHB][hapmap];0.88[JPT][hapmap];0.85[YRI][hapmap]
rs10971599	1.00[JPT][hapmap];0.82[YRI][hapmap];0.83[ASN][1000 genomes]
rs10971661	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs10971665	0.88[CEU][hapmap];0.90[CHB][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10971685	0.92[CEU][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12002215	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs12115798	0.89[CHB][hapmap];0.88[JPT][hapmap]
rs12335763	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12337095	0.82[CHB][hapmap]
rs12340535	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs12341652	0.91[CHB][hapmap];0.89[JPT][hapmap]
rs12341737	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs12346432	0.91[CHB][hapmap];0.89[JPT][hapmap];0.82[ASN][1000 genomes]
rs12347068	1.00[JPT][hapmap];0.82[YRI][hapmap]
rs12554323	0.89[CHB][hapmap];0.88[JPT][hapmap]
rs13283163	0.89[CHB][hapmap]
rs13286511	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs13290412	0.91[CHB][hapmap];0.89[JPT][hapmap]
rs13298219	0.90[CHB][hapmap];0.89[JPT][hapmap]
rs13300358	0.80[CHB][hapmap];0.89[JPT][hapmap]
rs13302664	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs13302841	0.88[JPT][hapmap]
rs1348369	0.94[CEU][hapmap];0.92[EUR][1000 genomes]
rs16917371	1.00[JPT][hapmap]
rs16924266	0.80[CHB][hapmap];0.89[JPT][hapmap]
rs1998976	1.00[CHB][hapmap];0.88[JPT][hapmap];0.80[ASN][1000 genomes]
rs2000216	0.94[CEU][hapmap];0.96[EUR][1000 genomes]
rs34233417	0.82[ASN][1000 genomes]
rs35244433	0.85[ASN][1000 genomes]
rs35945655	0.94[ASN][1000 genomes]
rs3758196	1.00[CHB][hapmap];0.88[JPT][hapmap];0.82[ASN][1000 genomes]
rs4237147	0.83[CEU][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs66463406	0.96[ASN][1000 genomes]
rs7021584	0.89[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.83[ASN][1000 genomes]
rs7022682	0.82[JPT][hapmap]
rs7022711	0.94[CEU][hapmap];0.93[YRI][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7024933	1.00[CEU][hapmap];0.93[YRI][hapmap];0.95[EUR][1000 genomes]
rs7026530	1.00[JPT][hapmap]
rs7028812	0.88[JPT][hapmap]
rs7029544	1.00[JPT][hapmap]
rs7041836	1.00[CHB][hapmap];0.89[JPT][hapmap];0.98[ASN][1000 genomes]
rs7043493	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs7045360	1.00[JPT][hapmap]
rs768485	0.89[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.83[ASN][1000 genomes]
rs7850570	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7853728	0.80[CHB][hapmap]
rs7864459	0.89[CHB][hapmap];0.88[JPT][hapmap]
rs7869854	0.88[JPT][hapmap]
rs7875889	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs9298952	1.00[JPT][hapmap];0.82[YRI][hapmap];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv892086	chr9:3012276-3410838	Bivalent Enhancer ZNF genes & repeats Strong transcription Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv1032921	chr9:3139007-3502815	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv539940	chr9:3139007-3502815	Strong transcription Weak transcription ZNF genes & repeats Enhancers Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv531566	chr9:3288211-3545454	Weak transcription Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
5	nsv892089	chr9:3290569-3578094	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
6	nsv916259	chr9:3308176-4296711	Enhancers ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
7	nsv1034280	chr9:3319718-3491987	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv539942	chr9:3319718-3491987	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	nsv1028815	chr9:3319718-3584455	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
10	nsv466091	chr9:3349487-3389660	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
11	nsv613146	chr9:3349487-3389660	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Strong transcription	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
12	nsv613147	chr9:3368111-3440355	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:3337800-3388800	Weak transcription	Primary T cells fromperipheralblood	blood
2	chr9:3341200-3397600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr9:3351000-3408200	Weak transcription	Fetal Intestine Small	intestine
4	chr9:3355000-3383800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr9:3359400-3383200	Weak transcription	Primary T cells from cord blood	blood
6	chr9:3359400-3387600	Weak transcription	Primary hematopoietic stem cells	blood
7	chr9:3359600-3383800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr9:3359800-3384000	Weak transcription	Primary B cells from cord blood	blood
9	chr9:3364200-3397200	Weak transcription	Left Ventricle	heart
10	chr9:3364800-3393800	Weak transcription	Adipose Nuclei	Adipose
11	chr9:3367600-3384800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr9:3367800-3383800	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr9:3369400-3398400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr9:3375800-3390200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr9:3377000-3386800	Weak transcription	Fetal Lung	lung
16	chr9:3377200-3390000	Weak transcription	Primary T helper cells fromperipheralblood	blood
17	chr9:3377400-3390400	Weak transcription	Primary B cells from peripheral blood	blood
18	chr9:3377600-3401400	Weak transcription	HMEC	breast
19	chr9:3377800-3401600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr9:3379800-3390400	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr9:3380400-3390400	Weak transcription	Thymus	Thymus
22	chr9:3380600-3391400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr9:3380800-3383400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr9:3381000-3397000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
25	chr9:3382200-3425000	Weak transcription	Aorta	Aorta
26	chr9:3382400-3384000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr9:3382400-3397000	Weak transcription	Fetal Intestine Large	intestine
28	chr9:3382400-3401400	Weak transcription	Brain Anterior Caudate	brain
29	chr9:3382800-3401000	Weak transcription	Brain Germinal Matrix	brain

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