Variant report

Variant	rs9596188
Chromosome Location	chr13:50318516-50318517
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:50268456..50270901-chr13:50317498..50319305,2	K562	blood:
2	chr13:50316640..50318955-chr13:50509690..50511603,2	MCF-7	breast:
3	chr13:50264386..50266994-chr13:50318266..50320898,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000123178	Chromatin interaction
ENSG00000123179	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs1043729	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12585921	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13313256	0.95[JPT][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17073322	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17073347	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17073356	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1819191	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1885723	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1986085	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1998363	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2181184	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2236326	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2407875	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];0.80[EUR][1000 genomes]
rs3736830	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs3742094	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3782929	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3903770	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];0.80[EUR][1000 genomes]
rs3990324	0.89[ASN][1000 genomes]
rs4941655	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4941656	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4942862	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4942865	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56738401	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs57118905	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs57783887	0.92[EUR][1000 genomes]
rs57794226	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58124341	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs60019803	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs60106669	0.92[EUR][1000 genomes]
rs60856213	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7318922	0.90[YRI][hapmap]
rs7321391	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7326885	0.81[AMR][1000 genomes]
rs7334018	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7335016	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7335310	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73483835	0.92[EUR][1000 genomes]
rs73485710	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs765291	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs765292	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7984711	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7989633	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7993631	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7993860	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7994062	0.95[AFR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7996015	0.88[YRI][hapmap]
rs8002212	0.90[YRI][hapmap]
rs9535306	0.83[ASN][1000 genomes]
rs9562911	0.95[JPT][hapmap]
rs9591288	0.80[YRI][hapmap]
rs9591293	0.87[AFR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9591294	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs9591296	0.86[JPT][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9596166	0.95[JPT][hapmap]
rs9596172	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9596173	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9596174	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9596175	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9596176	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9596181	0.84[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs9596189	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9596194	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv900072	chr13:50266109-50381016	Weak transcription ZNF genes & repeats Strong transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv900073	chr13:50286218-50381016	Enhancers Active TSS Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	esv1818134	chr13:50306897-50374102	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv900074	chr13:50317104-50381016	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:50266400-50349000	Weak transcription	Esophagus	oesophagus
2	chr13:50273200-50326000	Weak transcription	Aorta	Aorta
3	chr13:50273200-50333800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr13:50290000-50324000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr13:50290000-50334000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr13:50293200-50326000	Weak transcription	Fetal Brain Male	brain
7	chr13:50294200-50324000	Weak transcription	Rectal Smooth Muscle	rectum
8	chr13:50294400-50333000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr13:50296200-50330400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr13:50296400-50320200	Weak transcription	Spleen	Spleen
11	chr13:50296600-50330400	Weak transcription	Small Intestine	intestine
12	chr13:50296600-50338600	Weak transcription	Ovary	ovary
13	chr13:50297000-50322400	Weak transcription	Brain Cingulate Gyrus	brain
14	chr13:50298000-50327600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr13:50299200-50327600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr13:50299400-50319400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr13:50300600-50345600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr13:50300800-50321800	Weak transcription	Brain Anterior Caudate	brain
19	chr13:50301000-50319200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr13:50301200-50323600	Weak transcription	Colon Smooth Muscle	Colon
21	chr13:50301200-50327800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
22	chr13:50302800-50333800	Weak transcription	Thymus	Thymus
23	chr13:50303200-50319400	Weak transcription	Primary neutrophils fromperipheralblood	blood
24	chr13:50303200-50334000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr13:50304400-50321400	Weak transcription	Duodenum Mucosa	Duodenum
26	chr13:50305600-50319400	Weak transcription	Fetal Intestine Small	intestine
27	chr13:50305600-50319600	Weak transcription	Fetal Stomach	stomach
28	chr13:50305800-50319400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr13:50305800-50320200	Weak transcription	Fetal Muscle Leg	muscle
30	chr13:50306000-50319000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
31	chr13:50306000-50320200	Weak transcription	Stomach Smooth Muscle	stomach
32	chr13:50306000-50324000	Weak transcription	HSMMtube	muscle
33	chr13:50306000-50351600	Weak transcription	Rectal Mucosa Donor 29	rectum
34	chr13:50306200-50323200	Weak transcription	Brain Germinal Matrix	brain
35	chr13:50306200-50334200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr13:50306200-50336200	Weak transcription	Adipose Nuclei	Adipose
37	chr13:50306600-50319000	Weak transcription	Osteobl	bone
38	chr13:50306600-50323200	Weak transcription	NHEK	skin
39	chr13:50306800-50319000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr13:50306800-50333800	Weak transcription	H1 Cell Line	embryonic stem cell
41	chr13:50308000-50318800	Weak transcription	Primary T helper cells PMA-I stimulated	--
42	chr13:50308000-50320000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr13:50308000-50320600	Weak transcription	A549	lung
44	chr13:50308000-50356000	Weak transcription	Fetal Kidney	kidney
45	chr13:50308200-50319000	Weak transcription	Fetal Lung	lung
46	chr13:50308200-50319400	Weak transcription	Left Ventricle	heart
47	chr13:50308200-50319600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr13:50308200-50320200	Weak transcription	Brain Hippocampus Middle	brain
49	chr13:50308200-50321400	Weak transcription	Brain Substantia Nigra	brain
50	chr13:50308200-50324000	Weak transcription	Skeletal Muscle Female	skeletal muscle

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