Variant report

Variant	rs2797519
Chromosome Location	chr9:5785638-5785639
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:5627527..5629404-chr9:5785227..5787445,2	MCF-7	breast:
2	chr9:5784098..5787318-chr9:5787843..5791825,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000107036	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10733517	1.00[TSI][hapmap]
rs10975340	1.00[EUR][1000 genomes]
rs1141025	1.00[EUR][1000 genomes]
rs1260128	1.00[EUR][1000 genomes]
rs1260130	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs1260132	1.00[EUR][1000 genomes]
rs1260134	1.00[EUR][1000 genomes]
rs1260135	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1745887	1.00[EUR][1000 genomes]
rs1776008	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs2150703	1.00[TSI][hapmap]
rs2476262	1.00[EUR][1000 genomes]
rs2760408	1.00[EUR][1000 genomes]
rs2760409	1.00[EUR][1000 genomes]
rs2760410	1.00[EUR][1000 genomes]
rs2797512	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs2797514	1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2797516	1.00[EUR][1000 genomes]
rs3739649	1.00[TSI][hapmap]
rs4742131	1.00[TSI][hapmap]
rs58370080	1.00[EUR][1000 genomes]
rs6477001	1.00[EUR][1000 genomes]
rs6477002	1.00[EUR][1000 genomes]
rs7024130	1.00[TSI][hapmap]
rs7034210	1.00[TSI][hapmap]
rs7037680	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs7042100	1.00[EUR][1000 genomes]
rs7046793	1.00[EUR][1000 genomes]
rs73377834	1.00[EUR][1000 genomes]
rs73390661	1.00[AMR][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	nsv1017103	chr9:5509431-5987907	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv539965	chr9:5509431-5987907	ZNF genes & repeats Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv1019444	chr9:5598677-5807009	Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
4	nsv892151	chr9:5602528-5841438	Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
5	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
6	esv3331803	chr9:5766129-5905103	Weak transcription Enhancers Bivalent/Poised TSS Genic enhancers Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2797519	AHSP	trans	lymphoblastoid	seeQTL

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:5775000-5797000	Weak transcription	Psoas Muscle	Psoas
2	chr9:5779000-5792800	Strong transcription	Rectal Mucosa Donor 31	rectum
3	chr9:5779000-5793000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr9:5779200-5790800	Strong transcription	Primary T cells from cord blood	blood
5	chr9:5779200-5792800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr9:5779200-5809600	Weak transcription	NHDF-Ad	bronchial
7	chr9:5779200-5832200	Weak transcription	Fetal Brain Male	brain
8	chr9:5779600-5789000	Weak transcription	NH-A	brain
9	chr9:5779600-5814000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr9:5779600-5827800	Weak transcription	Small Intestine	intestine
11	chr9:5780400-5785800	Weak transcription	Colonic Mucosa	Colon
12	chr9:5780400-5786200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr9:5780400-5786400	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr9:5780400-5786400	Weak transcription	Spleen	Spleen
15	chr9:5780400-5788400	Strong transcription	Duodenum Mucosa	Duodenum
16	chr9:5780400-5788800	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr9:5780400-5789600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr9:5780400-5789600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr9:5780400-5793200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
20	chr9:5780400-5794200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr9:5780600-5785800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr9:5780600-5785800	Weak transcription	Thymus	Thymus
23	chr9:5780600-5786000	Weak transcription	Brain Substantia Nigra	brain
24	chr9:5780600-5786000	Weak transcription	Esophagus	oesophagus
25	chr9:5780600-5786000	Weak transcription	Lung	lung
26	chr9:5780600-5786000	Weak transcription	Stomach Smooth Muscle	stomach
27	chr9:5780600-5786200	Weak transcription	Rectal Smooth Muscle	rectum
28	chr9:5780600-5786400	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr9:5780600-5787200	Weak transcription	Fetal Intestine Small	intestine
30	chr9:5780600-5789600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr9:5780600-5792000	Weak transcription	Right Ventricle	heart
32	chr9:5780600-5799400	Weak transcription	Osteobl	bone
33	chr9:5780800-5785800	Weak transcription	Placenta	Placenta
34	chr9:5780800-5785800	Weak transcription	HSMM	muscle
35	chr9:5780800-5786000	Weak transcription	NHEK	skin
36	chr9:5780800-5786400	Weak transcription	Colon Smooth Muscle	Colon
37	chr9:5780800-5786400	Weak transcription	Ovary	ovary
38	chr9:5780800-5786600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr9:5780800-5786600	Weak transcription	K562	blood
40	chr9:5780800-5786600	Weak transcription	NHLF	lung
41	chr9:5780800-5787000	Weak transcription	Stomach Mucosa	stomach
42	chr9:5780800-5788600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr9:5780800-5790200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr9:5780800-5791200	Weak transcription	HSMMtube	muscle
45	chr9:5781000-5786400	Weak transcription	H1 Cell Line	embryonic stem cell
46	chr9:5781000-5786400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr9:5781000-5799400	Weak transcription	Muscle Satellite Cultured Cells	--
48	chr9:5781600-5786400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr9:5781800-5785800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr9:5781800-5786200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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