Variant report

Variant	rs7861549
Chromosome Location	chr9:2824677-2824678
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 14 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs61732412	1.00[AMR][1000 genomes]
rs7849647	1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7854605	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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	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
7	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
8	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
9	nsv1028011	chr9:2759097-2904277	Enhancers Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
10	nsv1022873	chr9:2768825-2863264	Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
11	nsv892083	chr9:2809548-2900651	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7861549	SLC12A7	trans	lymphoblastoid	seeQTL
rs7861549	GAS2	trans	lymphoblastoid	seeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:2793200-2826600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr9:2798000-2837400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr9:2801200-2838600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr9:2801600-2837200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr9:2803600-2829200	Weak transcription	Small Intestine	intestine
6	chr9:2805800-2829400	Weak transcription	Fetal Brain Male	brain
7	chr9:2808800-2827000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr9:2810400-2827400	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr9:2811600-2826200	Weak transcription	Primary neutrophils fromperipheralblood	blood
10	chr9:2811600-2826200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr9:2811600-2826200	Weak transcription	Brain Germinal Matrix	brain
12	chr9:2811600-2827600	Weak transcription	Gastric	stomach
13	chr9:2811600-2827600	Weak transcription	Right Ventricle	heart
14	chr9:2811600-2827600	Weak transcription	Thymus	Thymus
15	chr9:2811600-2827600	Weak transcription	Spleen	Spleen
16	chr9:2811600-2827800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr9:2811600-2827800	Weak transcription	Fetal Intestine Small	intestine
18	chr9:2811600-2828000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr9:2811600-2828200	Weak transcription	Colonic Mucosa	Colon
20	chr9:2811600-2842800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr9:2812200-2827600	Weak transcription	Lung	lung
22	chr9:2812200-2829000	Weak transcription	Brain Angular Gyrus	brain
23	chr9:2813000-2826400	Weak transcription	Brain Hippocampus Middle	brain
24	chr9:2813200-2827400	Weak transcription	Brain Substantia Nigra	brain
25	chr9:2813200-2828800	Weak transcription	Brain Cingulate Gyrus	brain
26	chr9:2814000-2827600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr9:2814000-2827600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr9:2814000-2828000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr9:2814000-2828800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
30	chr9:2814800-2838200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr9:2815200-2837200	Strong transcription	HMEC	breast
32	chr9:2815200-2837400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr9:2815600-2838200	Strong transcription	Primary T helper cells PMA-I stimulated	--
34	chr9:2815800-2837400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr9:2815800-2837800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr9:2816200-2827000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr9:2816800-2829200	Weak transcription	Pancreas	Pancrea
38	chr9:2818200-2828000	Weak transcription	Aorta	Aorta
39	chr9:2818200-2837400	Strong transcription	Rectal Mucosa Donor 31	rectum
40	chr9:2818800-2826200	Weak transcription	Stomach Smooth Muscle	stomach
41	chr9:2818800-2829200	Weak transcription	Stomach Mucosa	stomach
42	chr9:2819000-2827000	Weak transcription	Colon Smooth Muscle	Colon
43	chr9:2819000-2828400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
44	chr9:2819000-2828800	Weak transcription	Rectal Smooth Muscle	rectum
45	chr9:2819600-2825600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
46	chr9:2819600-2838200	Weak transcription	Fetal Heart	heart
47	chr9:2819600-2841800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
48	chr9:2820000-2837200	Weak transcription	Pancreatic Islets	Pancreatic Islet
49	chr9:2820200-2837800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr9:2822200-2825800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood

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