Variant report

Variant	rs2073829
Chromosome Location	chr9:136826457-136826458
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:136822394..136827953-chr9:136855901..136860268,9	MCF-7	breast:
2	chr9:136818593..136821583-chr9:136825689..136827854,2	MCF-7	breast:
3	chr9:136823911..136827460-chr9:136829913..136836528,5	MCF-7	breast:
4	chr9:136810410..136813300-chr9:136824316..136826699,2	MCF-7	breast:
5	chr9:136824147..136826582-chr9:136846037..136848091,2	MCF-7	breast:
6	chr9:136647018..136648853-chr9:136824302..136826935,2	MCF-7	breast:
7	chr9:136737400..136743457-chr9:136819359..136829756,12	MCF-7	breast:
8	chr9:136825997..136828565-chr9:136829281..136832020,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000160293	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs2073884	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2428005	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2519106	0.82[JPT][hapmap]
rs2519107	0.82[JPT][hapmap]
rs2519108	0.82[JPT][hapmap]
rs2519109	0.82[JPT][hapmap]
rs2519112	0.82[JPT][hapmap]
rs2519114	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2519796	1.00[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];0.93[CHD][hapmap];0.89[GIH][hapmap];0.94[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2519797	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2519799	0.82[JPT][hapmap]
rs2519807	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2519810	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2519822	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2789857	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2789858	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2789859	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2789860	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2789862	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2810531	0.80[JPT][hapmap]
rs2810534	0.81[JPT][hapmap]
rs2810537	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs886018	0.82[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv894123	chr9:136682408-136852501	Weak transcription Enhancers Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv894124	chr9:136716399-136870787	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	nsv894125	chr9:136723520-136931957	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv894128	chr9:136753246-136906752	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
5	nsv1046310	chr9:136762829-136872226	Enhancers Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv894130	chr9:136767346-136906752	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
7	nsv831748	chr9:136788484-136944326	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
8	nsv894131	chr9:136792765-136906752	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
9	nsv466626	chr9:136807770-136835343	Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
10	nsv615742	chr9:136807770-136835343	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
11	nsv831749	chr9:136809200-136915764	Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
12	nsv894132	chr9:136813341-136950691	Active TSS Genic enhancers Weak transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
13	nsv982642	chr9:136819005-136837069	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
14	nsv428226	chr9:136825035-136994606	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2073829	ABL1	cis	parietal	SCAN
rs2073829	C9orf98	cis	cerebellum	SCAN

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:136821800-136828600	Enhancers	Primary B cells from cord blood	blood
2	chr9:136822400-136828800	Enhancers	Primary B cells from peripheral blood	blood
3	chr9:136822600-136837000	Weak transcription	Colon Smooth Muscle	Colon
4	chr9:136822800-136828200	Weak transcription	Primary T helper cells fromperipheralblood	blood
5	chr9:136822800-136836600	Weak transcription	NHDF-Ad	bronchial
6	chr9:136823000-136827600	Enhancers	HUES6 Cell Line	embryonic stem cell
7	chr9:136823000-136829000	Weak transcription	Fetal Brain Female	brain
8	chr9:136823600-136826800	Enhancers	Duodenum Mucosa	Duodenum
9	chr9:136823600-136827000	Enhancers	HUES48 Cell Line	embryonic stem cell
10	chr9:136823600-136827000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr9:136823600-136827000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr9:136823600-136827200	Enhancers	H1 Cell Line	embryonic stem cell
13	chr9:136823600-136827200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr9:136823600-136827200	Enhancers	Primary hematopoietic stem cells short term culture	blood
15	chr9:136823600-136827200	Enhancers	Cortex derived primary cultured neurospheres	brain
16	chr9:136823600-136827200	Enhancers	Rectal Mucosa Donor 29	rectum
17	chr9:136823600-136827400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr9:136823600-136827400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr9:136823600-136827400	Enhancers	iPS-18 Cell Line	embryonic stem cell
20	chr9:136823600-136827400	Enhancers	Breast Myoepithelial Primary Cells	Breast
21	chr9:136823600-136827400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
22	chr9:136823600-136827400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr9:136823600-136827400	Enhancers	Placenta Amnion	Placenta Amnion
24	chr9:136823600-136827600	Enhancers	Lung	lung
25	chr9:136823600-136828800	Enhancers	Fetal Muscle Leg	muscle
26	chr9:136823600-136828800	Enhancers	Pancreas	Pancrea
27	chr9:136823800-136827200	Enhancers	Primary monocytes fromperipheralblood	blood
28	chr9:136823800-136827200	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
29	chr9:136823800-136827400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr9:136823800-136827600	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr9:136823800-136827600	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
32	chr9:136823800-136828400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr9:136823800-136829000	Enhancers	Stomach Mucosa	stomach
34	chr9:136824000-136826800	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr9:136824000-136826800	Enhancers	Sigmoid Colon	Sigmoid Colon
36	chr9:136824000-136827000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr9:136824000-136827200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
38	chr9:136824000-136827600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
39	chr9:136824200-136828800	Enhancers	Liver	Liver
40	chr9:136824400-136827200	Bivalent Enhancer	Placenta	Placenta
41	chr9:136824400-136836800	Weak transcription	NH-A	brain
42	chr9:136824600-136826600	Enhancers	Brain Inferior Temporal Lobe	brain
43	chr9:136824600-136827800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr9:136824800-136827600	Enhancers	Spleen	Spleen
45	chr9:136824800-136832200	Weak transcription	HSMMtube	muscle
46	chr9:136824800-136835800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr9:136825000-136826800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr9:136825000-136827000	Enhancers	NHEK	skin
49	chr9:136825000-136827600	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
50	chr9:136825200-136827400	Enhancers	Adipose Nuclei	Adipose

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