Variant report

Variant	rs16929629
Chromosome Location	chr9:12822458-12822459
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:12816711..12819917-chr9:12821131..12823680,3	MCF-7	breast:
2	chr9:12774109..12791345-chr9:12812800..12822770,37	MCF-7	breast:
3	chr9:12816957..12819670-chr9:12821766..12823551,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000153714	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10960809	0.95[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.88[ASN][1000 genomes]
rs10960810	0.94[CHB][hapmap];0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs10960811	0.95[CHB][hapmap];0.91[JPT][hapmap]
rs4111024	0.90[CHB][hapmap];0.90[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.86[ASN][1000 genomes]
rs6474734	0.89[CHB][hapmap];0.88[CHD][hapmap];0.89[GIH][hapmap];0.91[JPT][hapmap];0.80[MEX][hapmap];0.90[ASN][1000 genomes]
rs6474735	0.95[CHB][hapmap];0.91[JPT][hapmap];0.92[ASN][1000 genomes]
rs7049208	0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs7875509	0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv498136	chr9:12387840-12984158	Genic enhancers Enhancers Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
2	esv2422212	chr9:12448789-13127738	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	nsv1030835	chr9:12717405-12840928	Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv892573	chr9:12730636-12874703	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription 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	10 gene(s)	inside rSNPs	diseases
5	nsv892574	chr9:12754969-12918226	Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
6	nsv892575	chr9:12804243-12852462	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:12814600-12824800	Weak transcription	Psoas Muscle	Psoas
2	chr9:12814800-12823200	Weak transcription	Colonic Mucosa	Colon
3	chr9:12816200-12832000	Weak transcription	HSMMtube	muscle
4	chr9:12818000-12825000	Weak transcription	Fetal Muscle Trunk	muscle
5	chr9:12818000-12828800	Weak transcription	NHEK	skin
6	chr9:12818800-12822800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr9:12818800-12826000	Weak transcription	Gastric	stomach
8	chr9:12819000-12825600	Weak transcription	Aorta	Aorta
9	chr9:12819200-12823200	Weak transcription	Fetal Kidney	kidney
10	chr9:12819200-12825000	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr9:12819200-12825600	Weak transcription	Liver	Liver
12	chr9:12819200-12826400	Weak transcription	Colon Smooth Muscle	Colon
13	chr9:12819200-12826400	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr9:12819200-12826400	Weak transcription	Small Intestine	intestine
15	chr9:12819200-12827600	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr9:12819400-12825200	Weak transcription	Adipose Nuclei	Adipose
17	chr9:12819400-12826000	Weak transcription	Rectal Smooth Muscle	rectum
18	chr9:12819400-12828600	Weak transcription	Stomach Smooth Muscle	stomach
19	chr9:12819800-12831400	Weak transcription	Fetal Intestine Small	intestine
20	chr9:12820000-12823200	Strong transcription	Fetal Lung	lung
21	chr9:12820000-12830600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr9:12820200-12825000	Weak transcription	HepG2	liver
23	chr9:12820400-12826200	Weak transcription	Fetal Stomach	stomach
24	chr9:12821200-12822600	Enhancers	NHDF-Ad	bronchial
25	chr9:12821400-12822800	Genic enhancers	Osteobl	bone
26	chr9:12821400-12823600	Strong transcription	Fetal Intestine Large	intestine
27	chr9:12821400-12823800	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr9:12821400-12823800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr9:12821400-12825200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr9:12821600-12822800	Enhancers	Muscle Satellite Cultured Cells	--
31	chr9:12821600-12827000	Weak transcription	A549	lung
32	chr9:12821800-12823400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr9:12821800-12824800	Weak transcription	Fetal Muscle Leg	muscle
34	chr9:12821800-12825000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr9:12821800-12825400	Weak transcription	Pancreas	Pancrea
36	chr9:12821800-12825800	Weak transcription	NHLF	lung
37	chr9:12821800-12826400	Weak transcription	Lung	lung
38	chr9:12821800-12827600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr9:12821800-12828400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr9:12822000-12822600	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr9:12822000-12823200	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr9:12822200-12828600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr9:12822400-12825400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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