Variant report

Variant	rs11144996
Chromosome Location	chr9:79271509-79271510
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	chr9:79082022..79083727-chr9:79271380..79273433,2	MCF-7	breast:
2	chr9:79073700..79075810-chr9:79270098..79272693,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000187210	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10521475	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11144986	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11144987	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.94[ASN][1000 genomes]
rs11144992	1.00[CEU][hapmap];0.92[CHB][hapmap];0.90[JPT][hapmap];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17062768	1.00[CEU][hapmap]
rs17062772	1.00[CEU][hapmap]
rs17062775	1.00[CEU][hapmap]
rs17062778	1.00[CEU][hapmap]
rs17062858	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.92[GIH][hapmap];0.91[JPT][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1854441	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.92[GIH][hapmap];0.91[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1952460	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.94[ASN][1000 genomes]
rs2067501	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.94[ASN][1000 genomes]
rs499746	1.00[CEU][hapmap]
rs57389265	0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs634063	0.93[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs637207	1.00[CEU][hapmap]
rs644893	1.00[CEU][hapmap]
rs7027074	0.94[ASN][1000 genomes]
rs7028756	0.94[ASN][1000 genomes]
rs7038619	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.94[ASN][1000 genomes]
rs7039310	1.00[CHB][hapmap];0.90[JPT][hapmap];0.95[ASN][1000 genomes]
rs7045505	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.83[GIH][hapmap];0.90[JPT][hapmap];0.94[ASN][1000 genomes]
rs7847922	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7859873	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869152	chr9:78742197-79583399	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv931033	chr9:78850330-79366454	Genic enhancers Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv893479	chr9:78971253-79275226	Weak transcription Strong transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	nsv949417	chr9:79078703-79282589	Strong transcription Genic enhancers Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
5	nsv1040363	chr9:79246366-79711737	Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:79252600-79278000	Weak transcription	Gastric	stomach
2	chr9:79259000-79278000	Weak transcription	Spleen	Spleen
3	chr9:79260000-79282400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr9:79263600-79272800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr9:79263600-79282200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr9:79265600-79274000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr9:79266000-79278000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr9:79266400-79272000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr9:79266400-79306800	Weak transcription	Fetal Stomach	stomach
10	chr9:79266600-79274200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr9:79266600-79282200	Weak transcription	Brain Anterior Caudate	brain
12	chr9:79266800-79272600	Enhancers	Primary hematopoietic stem cells	blood
13	chr9:79267000-79271600	Weak transcription	Primary T cells fromperipheralblood	blood
14	chr9:79267000-79271800	Weak transcription	Primary T helper cells PMA-I stimulated	--
15	chr9:79267000-79273200	Weak transcription	Duodenum Mucosa	Duodenum
16	chr9:79267200-79273400	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr9:79267600-79273400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr9:79268000-79272600	Enhancers	Primary hematopoietic stem cells short term culture	blood
19	chr9:79268200-79273400	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr9:79268400-79272600	Enhancers	NHDF-Ad	bronchial
21	chr9:79268800-79272000	Enhancers	Stomach Mucosa	stomach
22	chr9:79268800-79273400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr9:79269000-79278000	Weak transcription	Aorta	Aorta
24	chr9:79269200-79273200	Weak transcription	Fetal Intestine Small	intestine
25	chr9:79269200-79273400	Weak transcription	Fetal Kidney	kidney
26	chr9:79269200-79275800	Weak transcription	Fetal Muscle Leg	muscle
27	chr9:79269400-79274000	Enhancers	Muscle Satellite Cultured Cells	--
28	chr9:79269400-79277000	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr9:79269800-79272200	Strong transcription	Stomach Smooth Muscle	stomach
30	chr9:79269800-79272800	Enhancers	Pancreatic Islets	Pancreatic Islet
31	chr9:79269800-79282200	Weak transcription	Brain Substantia Nigra	brain
32	chr9:79270000-79271800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
33	chr9:79270200-79272200	Weak transcription	Primary B cells from cord blood	blood
34	chr9:79270400-79271600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr9:79270400-79271600	Weak transcription	Primary B cells from peripheral blood	blood
36	chr9:79270400-79271600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
37	chr9:79270400-79271600	Enhancers	Osteobl	bone
38	chr9:79270400-79271800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
39	chr9:79270400-79272000	Genic enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr9:79270400-79272800	Enhancers	HUVEC	blood vessel
41	chr9:79270400-79273800	Weak transcription	Brain Hippocampus Middle	brain
42	chr9:79270400-79277000	Weak transcription	Duodenum Smooth Muscle	Duodenum
43	chr9:79270400-79277200	Weak transcription	GM12878-XiMat	blood
44	chr9:79270400-79303000	Weak transcription	Colon Smooth Muscle	Colon
45	chr9:79270600-79271600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr9:79270600-79271800	Weak transcription	NHLF	lung
47	chr9:79270600-79272800	Enhancers	NH-A	brain
48	chr9:79270600-79273400	Weak transcription	Primary monocytes fromperipheralblood	blood
49	chr9:79270600-79273400	Weak transcription	Fetal Thymus	thymus
50	chr9:79270600-79273800	Weak transcription	HUES48 Cell Line	embryonic stem cell

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