Variant report

Variant	rs9844178
Chromosome Location	chr3:52375359-52375360
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:52361669..52364614-chr3:52373969..52375582,2	K562	blood:
2	chr3:52375220..52376808-chr3:52378579..52380565,2	MCF-7	breast:

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

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

rs_ID	r²[population]
rs10212560	1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10440116	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[EUR][1000 genomes]
rs10865972	0.90[LWK][hapmap];1.00[YRI][hapmap]
rs13318570	1.00[AMR][1000 genomes]
rs1541495	0.90[LWK][hapmap];1.00[YRI][hapmap]
rs17052143	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28413740	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28434358	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28636773	1.00[EUR][1000 genomes]
rs34540591	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4687614	0.90[LWK][hapmap];1.00[YRI][hapmap]
rs5743834	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs9813448	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9813468	1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9813489	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs9813653	1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9814016	1.00[EUR][1000 genomes]
rs9815559	1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9821916	1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9824342	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9828432	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9828488	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9831689	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9834363	1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9834919	1.00[EUR][1000 genomes]
rs9836166	1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9842960	0.88[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[EUR][1000 genomes]
rs9843055	1.00[ASW][hapmap];0.81[LWK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9845752	1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9857947	1.00[EUR][1000 genomes]
rs9863874	0.82[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs9868332	1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[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	nsv834695	chr3:52199701-52400577	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	98 gene(s)	inside rSNPs	diseases
2	nsv876789	chr3:52247110-52575831	Flanking Active TSS Bivalent Enhancer Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
3	nsv984542	chr3:52285682-52516115	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	94 gene(s)	inside rSNPs	diseases
4	nsv834696	chr3:52317478-52479537	Flanking Active TSS Active TSS Strong transcription Weak transcription Bivalent Enhancer Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	45 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52330400-52378600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr3:52344600-52378600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
3	chr3:52352000-52379800	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr3:52352200-52379000	Weak transcription	Colonic Mucosa	Colon
5	chr3:52352200-52382000	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr3:52352200-52384600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr3:52352600-52379400	Weak transcription	Pancreas	Pancrea
8	chr3:52353400-52377400	Weak transcription	Fetal Muscle Leg	muscle
9	chr3:52354400-52379800	Weak transcription	Esophagus	oesophagus
10	chr3:52354800-52384000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr3:52358400-52380400	Weak transcription	Ovary	ovary
12	chr3:52360400-52376200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr3:52362400-52378200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr3:52362800-52378600	Weak transcription	Brain Cingulate Gyrus	brain
15	chr3:52364200-52375800	Weak transcription	GM12878-XiMat	blood
16	chr3:52364200-52383000	Weak transcription	Fetal Lung	lung
17	chr3:52364400-52379400	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr3:52364800-52394400	Weak transcription	HSMMtube	muscle
19	chr3:52366400-52378400	Weak transcription	Brain Anterior Caudate	brain
20	chr3:52366400-52383000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr3:52366600-52377800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
22	chr3:52366600-52377800	Weak transcription	Spleen	Spleen
23	chr3:52366600-52378400	Weak transcription	Gastric	stomach
24	chr3:52366600-52379400	Weak transcription	Stomach Smooth Muscle	stomach
25	chr3:52366600-52386600	Weak transcription	Aorta	Aorta
26	chr3:52366800-52383000	Weak transcription	Rectal Smooth Muscle	rectum
27	chr3:52367200-52378600	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr3:52367200-52379600	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr3:52367600-52384400	Weak transcription	Fetal Kidney	kidney
30	chr3:52367800-52375800	Weak transcription	Fetal Stomach	stomach
31	chr3:52368400-52376200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr3:52368400-52378400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
33	chr3:52368400-52378400	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr3:52368400-52378600	Weak transcription	Primary B cells from peripheral blood	blood
35	chr3:52368400-52383000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
36	chr3:52368800-52377000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr3:52368800-52377400	Weak transcription	Adipose Nuclei	Adipose
38	chr3:52368800-52377600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr3:52368800-52378200	Weak transcription	Primary T helper cells PMA-I stimulated	--
40	chr3:52368800-52378200	Weak transcription	Fetal Muscle Trunk	muscle
41	chr3:52368800-52378400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr3:52368800-52380200	Weak transcription	Left Ventricle	heart
43	chr3:52368800-52380400	Weak transcription	Placenta	Placenta
44	chr3:52368800-52380400	Weak transcription	Rectal Mucosa Donor 29	rectum
45	chr3:52370600-52379600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr3:52370800-52377400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr3:52371000-52377400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr3:52372000-52379200	Weak transcription	Primary B cells from cord blood	blood
49	chr3:52372000-52379600	Weak transcription	NHLF	lung
50	chr3:52372000-52380400	Weak transcription	Primary hematopoietic stem cells	blood

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