Variant report

Variant	rs1411949
Chromosome Location	chr9:6012968-6012969
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:6006778..6010531-chr9:6011866..6018012,11	MCF-7	breast:

Variant related genes	Relation type
ENSG00000183354	Chromatin interaction
ENSG00000263575	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10116214	1.00[EUR][1000 genomes]
rs10125832	1.00[EUR][1000 genomes]
rs10975350	1.00[EUR][1000 genomes]
rs10975351	1.00[EUR][1000 genomes]
rs10975362	1.00[EUR][1000 genomes]
rs10975363	1.00[EUR][1000 genomes]
rs10975364	1.00[EUR][1000 genomes]
rs10975372	1.00[EUR][1000 genomes]
rs10975377	1.00[EUR][1000 genomes]
rs11506678	1.00[EUR][1000 genomes]
rs12337300	1.00[EUR][1000 genomes]
rs12337445	1.00[EUR][1000 genomes]
rs12337790	1.00[EUR][1000 genomes]
rs12339713	1.00[EUR][1000 genomes]
rs12339886	1.00[EUR][1000 genomes]
rs12339889	1.00[EUR][1000 genomes]
rs12340153	1.00[EUR][1000 genomes]
rs12340531	1.00[EUR][1000 genomes]
rs12341021	1.00[EUR][1000 genomes]
rs12342166	1.00[EUR][1000 genomes]
rs12342282	1.00[EUR][1000 genomes]
rs12343325	1.00[EUR][1000 genomes]
rs12345849	1.00[EUR][1000 genomes]
rs12351533	1.00[EUR][1000 genomes]
rs28431078	1.00[EUR][1000 genomes]
rs28706504	1.00[EUR][1000 genomes]
rs386775	1.00[EUR][1000 genomes]
rs57154492	1.00[EUR][1000 genomes]
rs58291302	1.00[EUR][1000 genomes]
rs60037728	1.00[EUR][1000 genomes]
rs7022080	1.00[EUR][1000 genomes]
rs7029847	1.00[EUR][1000 genomes]
rs73383109	1.00[EUR][1000 genomes]
rs73383113	1.00[EUR][1000 genomes]
rs73383114	1.00[EUR][1000 genomes]
rs73383144	1.00[EUR][1000 genomes]
rs73385128	1.00[EUR][1000 genomes]
rs73389036	1.00[EUR][1000 genomes]
rs73389044	1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs73397307	1.00[EUR][1000 genomes]
rs73397376	1.00[EUR][1000 genomes]
rs73399307	1.00[EUR][1000 genomes]
rs73639554	1.00[EUR][1000 genomes]
rs73639568	1.00[EUR][1000 genomes]
rs7854980	1.00[EUR][1000 genomes]
rs7858084	1.00[EUR][1000 genomes]
rs7858846	1.00[EUR][1000 genomes]
rs7875607	1.00[EUR][1000 genomes]
rs9299025	1.00[EUR][1000 genomes]

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	nsv948847	chr9:5712626-6417677	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv1031086	chr9:5806949-6630686	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
3	nsv539967	chr9:5806949-6630686	Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
4	nsv892155	chr9:5825768-6044937	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
5	nsv1015450	chr9:5915640-6114652	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
6	nsv824832	chr9:6010950-6014233	Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
7	nsv824833	chr9:6011129-6014118	Genic enhancers Weak transcription Strong transcription ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
8	nsv824834	chr9:6011129-6014233	Weak transcription Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
9	nsv824835	chr9:6011129-6014339	Strong transcription Weak transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
10	nsv824836	chr9:6011332-6014233	Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
11	nsv824837	chr9:6011419-6014118	Transcr. at gene 5' and 3' Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
12	esv18008	chr9:6011447-6014308	Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
13	nsv824838	chr9:6011798-6014414	Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Weak transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
14	nsv972646	chr9:6012519-6014296	Enhancers Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Strong transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:6008000-6014800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr9:6008400-6013400	Weak transcription	Gastric	stomach
3	chr9:6008400-6014200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr9:6008600-6013800	Weak transcription	Small Intestine	intestine
5	chr9:6008600-6014400	Weak transcription	Esophagus	oesophagus
6	chr9:6008600-6015200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr9:6008800-6013400	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr9:6008800-6014200	Weak transcription	Lung	lung
9	chr9:6008800-6014400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr9:6008800-6014400	Weak transcription	Colonic Mucosa	Colon
11	chr9:6008800-6014400	Weak transcription	Spleen	Spleen
12	chr9:6008800-6014600	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr9:6009000-6013600	Weak transcription	Aorta	Aorta
14	chr9:6009000-6013800	Weak transcription	Fetal Stomach	stomach
15	chr9:6009000-6014000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr9:6009000-6014200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr9:6009000-6014400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr9:6009000-6014400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr9:6009000-6014400	Weak transcription	Ovary	ovary
20	chr9:6009000-6014600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr9:6009200-6013200	Weak transcription	Brain Cingulate Gyrus	brain
22	chr9:6009200-6013200	Weak transcription	Rectal Smooth Muscle	rectum
23	chr9:6009200-6013200	Weak transcription	Thymus	Thymus
24	chr9:6009200-6013400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
25	chr9:6009200-6013600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr9:6009200-6013600	Weak transcription	Fetal Intestine Small	intestine
27	chr9:6009200-6013600	Weak transcription	Right Atrium	heart
28	chr9:6009200-6013600	Weak transcription	Stomach Smooth Muscle	stomach
29	chr9:6009200-6013800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr9:6009200-6014000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr9:6009200-6014200	Weak transcription	Brain Substantia Nigra	brain
32	chr9:6009200-6014200	Weak transcription	Colon Smooth Muscle	Colon
33	chr9:6009200-6014200	Weak transcription	Placenta Amnion	Placenta Amnion
34	chr9:6009200-6014400	Weak transcription	Primary neutrophils fromperipheralblood	blood
35	chr9:6009200-6014400	Weak transcription	Stomach Mucosa	stomach
36	chr9:6009400-6013000	Weak transcription	Primary T helper cells PMA-I stimulated	--
37	chr9:6009400-6013000	Weak transcription	Brain Hippocampus Middle	brain
38	chr9:6009400-6013000	Weak transcription	HMEC	breast
39	chr9:6009400-6013400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
40	chr9:6009400-6013400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
41	chr9:6009400-6013400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
42	chr9:6009400-6013600	Weak transcription	HSMMtube	muscle
43	chr9:6009400-6014200	Weak transcription	NHLF	lung
44	chr9:6009400-6014400	Weak transcription	Muscle Satellite Cultured Cells	--
45	chr9:6009600-6013400	Weak transcription	Rectal Mucosa Donor 29	rectum
46	chr9:6009800-6013400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
47	chr9:6009800-6014200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
48	chr9:6010200-6014000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
49	chr9:6010400-6014000	Strong transcription	Primary B cells from cord blood	blood
50	chr9:6010800-6014000	Strong transcription	HUES64 Cell Line	embryonic stem cell

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