Variant report

Variant	rs9878186
Chromosome Location	chr3:113218089-113218090
allele	C/T
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:6)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:113217243..113219124-chr3:113250664..113252376,2	MCF-7	breast:
2	chr3:113215849..113222351-chr3:113231718..113236655,12	MCF-7	breast:
3	chr3:113216822..113219310-chr3:113237513..113239458,2	MCF-7	breast:
4	chr3:113215914..113218639-chr3:113252642..113255587,3	MCF-7	breast:
5	chr3:113216065..113219439-chr3:113250291..113253077,5	MCF-7	breast:
6	chr3:113216951..113219431-chr3:113270962..113272792,3	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-WDR52-3	chr3:113217783-113218429	NONHSAT091231

No data

Variant related genes	Relation type
ENSG00000163611	Chromatin interaction
ENSG00000072858	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs13326562	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13327031	1.00[EUR][1000 genomes]
rs13353449	1.00[EUR][1000 genomes]
rs2399487	1.00[CEU][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28539944	0.81[EUR][1000 genomes]
rs28614095	0.81[EUR][1000 genomes]
rs4419353	1.00[CEU][hapmap];0.88[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6438154	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6763234	1.00[CEU][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6779241	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs6780720	1.00[CEU][hapmap];0.90[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6781507	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6797630	0.81[EUR][1000 genomes]
rs6808103	1.00[CEU][hapmap];0.90[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72950895	0.81[EUR][1000 genomes]
rs7612448	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs7618195	0.86[EUR][1000 genomes]
rs7625829	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs7629636	1.00[CEU][hapmap];0.89[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7645188	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9810059	1.00[CEU][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9810754	0.81[EUR][1000 genomes]
rs9811168	0.90[EUR][1000 genomes]
rs9827490	0.81[EUR][1000 genomes]
rs9827772	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs9836199	0.90[EUR][1000 genomes]
rs9846529	0.81[EUR][1000 genomes]
rs9851183	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9851407	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9852068	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs9860473	0.95[EUR][1000 genomes]
rs9863114	0.90[EUR][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	nsv1013506	chr3:112890608-113680951	Weak transcription Bivalent/Poised TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv1004000	chr3:113116778-113513899	Weak transcription Strong transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv877349	chr3:113208224-113323787	Enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
4	nsv877350	chr3:113208224-113332235	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:113160800-113224800	Weak transcription	Placenta	Placenta
2	chr3:113160800-113232600	Weak transcription	Right Ventricle	heart
3	chr3:113172800-113232800	Weak transcription	HSMMtube	muscle
4	chr3:113176400-113233200	Weak transcription	Gastric	stomach
5	chr3:113177400-113225800	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr3:113177600-113224400	Weak transcription	Spleen	Spleen
7	chr3:113179600-113232400	Weak transcription	Rectal Smooth Muscle	rectum
8	chr3:113179600-113232800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr3:113184000-113233200	Weak transcription	Pancreas	Pancrea
10	chr3:113187200-113224400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr3:113201400-113232600	Weak transcription	Brain Hippocampus Middle	brain
12	chr3:113202400-113232800	Weak transcription	Fetal Brain Female	brain
13	chr3:113203200-113223600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr3:113203400-113229200	Weak transcription	Lung	lung
15	chr3:113204000-113221200	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr3:113204000-113223400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr3:113204400-113224600	Weak transcription	Aorta	Aorta
18	chr3:113204400-113230600	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr3:113204600-113223000	Weak transcription	HepG2	liver
20	chr3:113204600-113232800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr3:113204600-113233200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr3:113204600-113233200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr3:113204600-113233200	Weak transcription	Esophagus	oesophagus
24	chr3:113204800-113221400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
25	chr3:113204800-113222400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr3:113204800-113232400	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr3:113204800-113232600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
28	chr3:113204800-113232800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr3:113204800-113233200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr3:113205000-113224200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr3:113205000-113224400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr3:113205200-113220600	Weak transcription	K562	blood
33	chr3:113207600-113232600	Weak transcription	NHEK	skin
34	chr3:113207600-113233000	Weak transcription	Psoas Muscle	Psoas
35	chr3:113207800-113233000	Weak transcription	H9 Cell Line	embryonic stem cell
36	chr3:113208200-113223800	Weak transcription	Skeletal Muscle Female	skeletal muscle
37	chr3:113209000-113232600	Weak transcription	Fetal Kidney	kidney
38	chr3:113209200-113232800	Weak transcription	H1 Cell Line	embryonic stem cell
39	chr3:113209400-113232800	Weak transcription	Stomach Mucosa	stomach
40	chr3:113209800-113228800	Weak transcription	Cortex derived primary cultured neurospheres	brain
41	chr3:113209800-113232800	Weak transcription	Brain Inferior Temporal Lobe	brain
42	chr3:113210000-113224400	Weak transcription	Thymus	Thymus
43	chr3:113210000-113233000	Weak transcription	HSMM	muscle
44	chr3:113210200-113220600	Weak transcription	Fetal Lung	lung
45	chr3:113210200-113233200	Weak transcription	Colonic Mucosa	Colon
46	chr3:113210400-113231600	Weak transcription	Fetal Intestine Small	intestine
47	chr3:113210400-113232600	Weak transcription	NHLF	lung
48	chr3:113212200-113232800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr3:113212400-113223800	Weak transcription	Primary hematopoietic stem cells	blood
50	chr3:113212400-113232600	Weak transcription	Brain Angular Gyrus	brain

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