Variant report

Variant	rs12352254
Chromosome Location	chr9:2729686-2729687
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 56 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1007021	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1007022	0.91[CEU][hapmap];1.00[CHB][hapmap];0.89[ASN][1000 genomes]
rs10511435	1.00[CHB][hapmap]
rs10812302	1.00[CHB][hapmap]
rs10966848	1.00[CHB][hapmap]
rs10967043	1.00[CHB][hapmap]
rs10967088	1.00[CHB][hapmap]
rs10967099	1.00[CHB][hapmap]
rs10967100	1.00[CHB][hapmap]
rs10967775	0.82[ASN][1000 genomes]
rs12341721	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12343218	1.00[CEU][hapmap];0.93[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes]
rs12348301	1.00[CHB][hapmap]
rs12352612	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12378635	1.00[CHB][hapmap]
rs12553678	1.00[CHB][hapmap]
rs13299915	1.00[CHB][hapmap]
rs1355640	1.00[CHB][hapmap]
rs1473839	1.00[CHB][hapmap]
rs1512713	1.00[CHB][hapmap]
rs16909365	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs17656045	1.00[CHB][hapmap]
rs17656056	1.00[CHB][hapmap]
rs17712447	1.00[CHB][hapmap]
rs17712459	1.00[CHB][hapmap]
rs2094967	1.00[CHB][hapmap]
rs2094968	1.00[CHB][hapmap]
rs2168136	1.00[CHB][hapmap]
rs41306094	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs41312842	1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs575205	1.00[CHB][hapmap]
rs60573542	0.83[EUR][1000 genomes]
rs7040984	1.00[CHB][hapmap]
rs73390710	0.85[EUR][1000 genomes]
rs7856406	0.83[EUR][1000 genomes]
rs7858086	1.00[CHB][hapmap]
rs7859924	1.00[EUR][1000 genomes]
rs7864004	1.00[CHB][hapmap]
rs986567	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530929	chr9:1998911-2925112	Active TSS Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv916750	chr9:2430846-2826706	Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	nsv1017581	chr9:2494815-3172020	Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv539934	chr9:2494815-3172020	Strong transcription Weak transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
5	nsv892079	chr9:2681430-2931341	Weak transcription Enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
6	nsv531565	chr9:2682523-2784028	Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv516425	chr9:2690980-2790307	ZNF genes & repeats Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv892081	chr9:2691186-2851026	Active TSS Genic enhancers Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
9	nsv1032667	chr9:2691667-2788242	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
10	nsv1019973	chr9:2691812-2790419	Strong transcription Enhancers Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
11	nsv539935	chr9:2691812-2790419	Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
12	nsv892082	chr9:2699606-2833267	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
13	nsv1021572	chr9:2703159-2790123	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
14	nsv1024262	chr9:2703159-3067931	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS 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 lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
15	nsv1032100	chr9:2720207-2766110	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
16	nsv1033982	chr9:2724666-2780665	ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
17	nsv539936	chr9:2724666-2780665	Strong transcription Enhancers ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

No data

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:2718000-2772800	Weak transcription	Aorta	Aorta
2	chr9:2719200-2768400	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr9:2719200-2768400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr9:2720600-2731800	Weak transcription	Primary T cells from cord blood	blood
5	chr9:2723200-2758000	Weak transcription	HSMM	muscle
6	chr9:2723200-2768400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr9:2724000-2735800	Weak transcription	HSMMtube	muscle
8	chr9:2724000-2746400	Weak transcription	NHEK	skin
9	chr9:2724800-2746200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr9:2725200-2730600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr9:2726200-2768400	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr9:2727000-2744600	Weak transcription	Spleen	Spleen
13	chr9:2727200-2733400	Weak transcription	Fetal Muscle Trunk	muscle
14	chr9:2727400-2732000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr9:2727800-2729800	Enhancers	Fetal Heart	heart
16	chr9:2727800-2733000	Enhancers	Ovary	ovary
17	chr9:2728200-2730600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr9:2728200-2731400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr9:2728200-2732000	Weak transcription	Right Atrium	heart
20	chr9:2728200-2732600	Weak transcription	Left Ventricle	heart
21	chr9:2728200-2746000	Weak transcription	Gastric	stomach
22	chr9:2728200-2755600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr9:2728200-2761200	Weak transcription	GM12878-XiMat	blood
24	chr9:2728200-2768400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr9:2728400-2731400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr9:2728400-2741400	Weak transcription	Fetal Muscle Leg	muscle
27	chr9:2728400-2745600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr9:2728400-2746000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr9:2728400-2746200	Weak transcription	HUES48 Cell Line	embryonic stem cell
30	chr9:2728400-2759400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr9:2728400-2759400	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr9:2728600-2735600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr9:2728600-2743800	Weak transcription	K562	blood
34	chr9:2728600-2746600	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr9:2728600-2746800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr9:2728600-2758800	Weak transcription	Fetal Lung	lung
37	chr9:2728600-2759200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr9:2728600-2768400	Weak transcription	Primary B cells from cord blood	blood
39	chr9:2728600-2772400	Weak transcription	Brain Hippocampus Middle	brain
40	chr9:2728800-2729800	Weak transcription	Fetal Kidney	kidney
41	chr9:2728800-2731400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr9:2728800-2745600	Weak transcription	HUES64 Cell Line	embryonic stem cell
43	chr9:2728800-2745800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
44	chr9:2728800-2750600	Weak transcription	HepG2	liver
45	chr9:2729000-2730000	Enhancers	NHDF-Ad	bronchial
46	chr9:2729000-2731000	Enhancers	Fetal Stomach	stomach
47	chr9:2729200-2745800	Weak transcription	Muscle Satellite Cultured Cells	--
48	chr9:2729200-2746000	Weak transcription	A549	lung
49	chr9:2729200-2768400	Weak transcription	NHLF	lung
50	chr9:2729200-2768800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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