Variant report

Variant	rs9829961
Chromosome Location	chr3:156406799-156406800
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:156391939..156394186-chr3:156406750..156409428,2	K562	blood:
2	chr3:156254995..156257951-chr3:156406375..156408006,2	K562	blood:
3	chr3:156342470..156344204-chr3:156404618..156406838,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000163659	Chromatin interaction
ENSG00000243926	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs13323819	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1397191	0.89[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16826731	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1991618	1.00[AMR][1000 genomes]
rs28695987	1.00[AMR][1000 genomes]
rs56231331	0.81[AFR][1000 genomes]
rs56234943	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57472927	1.00[AMR][1000 genomes]
rs60659904	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61607068	1.00[AMR][1000 genomes]
rs6763606	1.00[AMR][1000 genomes]
rs6779040	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6797924	1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73873709	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73873711	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7609776	1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7610539	1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7610749	1.00[AMR][1000 genomes]
rs7620352	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7620432	0.94[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7651446	0.89[YRI][hapmap];0.83[AFR][1000 genomes]
rs9814160	1.00[AMR][1000 genomes]
rs9834930	0.81[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9835232	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9837209	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9841118	1.00[AMR][1000 genomes]
rs9853712	1.00[AMR][1000 genomes]
rs9855517	1.00[AMR][1000 genomes]
rs9866769	1.00[AMR][1000 genomes]
rs9870674	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9873467	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9873640	1.00[AMR][1000 genomes]
rs9883478	1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014755	chr3:155889430-156411894	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Bivalent Enhancer 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	40 gene(s)	inside rSNPs	diseases
2	nsv428745	chr3:156405054-156577840	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:156394000-156436000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr3:156394200-156412600	Weak transcription	Placenta	Placenta
3	chr3:156394400-156411800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr3:156395600-156438600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr3:156395800-156408600	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr3:156396200-156407400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr3:156396400-156407400	Weak transcription	Esophagus	oesophagus
8	chr3:156396400-156407400	Weak transcription	Spleen	Spleen
9	chr3:156396400-156408800	Weak transcription	Colonic Mucosa	Colon
10	chr3:156396400-156413000	Weak transcription	Fetal Muscle Trunk	muscle
11	chr3:156396400-156414400	Weak transcription	Thymus	Thymus
12	chr3:156396400-156424800	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr3:156396600-156441000	Weak transcription	Lung	lung
14	chr3:156397800-156413000	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr3:156398400-156408800	Enhancers	Primary T helper cells fromperipheralblood	blood
16	chr3:156398600-156409600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
17	chr3:156399200-156407400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr3:156399200-156407400	Weak transcription	Fetal Intestine Large	intestine
19	chr3:156399200-156412400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr3:156399600-156407400	Weak transcription	Fetal Brain Female	brain
21	chr3:156399800-156407400	Weak transcription	Gastric	stomach
22	chr3:156399800-156408600	Genic enhancers	NHEK	skin
23	chr3:156399800-156410200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
24	chr3:156399800-156411200	Weak transcription	HUES48 Cell Line	embryonic stem cell
25	chr3:156399800-156411400	Weak transcription	Fetal Thymus	thymus
26	chr3:156399800-156411800	Enhancers	Brain Hippocampus Middle	brain
27	chr3:156399800-156413200	Weak transcription	Fetal Muscle Leg	muscle
28	chr3:156400000-156412200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
29	chr3:156400400-156411600	Weak transcription	Primary hematopoietic stem cells	blood
30	chr3:156401600-156409400	Enhancers	Primary T killer memory cells from peripheral blood	blood
31	chr3:156402600-156407400	Weak transcription	Right Atrium	heart
32	chr3:156402600-156410800	Enhancers	Liver	Liver
33	chr3:156402800-156409400	Enhancers	Fetal Heart	heart
34	chr3:156403000-156406800	Enhancers	HUVEC	blood vessel
35	chr3:156403400-156407400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
36	chr3:156403400-156409200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr3:156403400-156421800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
38	chr3:156403600-156408000	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr3:156403600-156409200	Weak transcription	HUES64 Cell Line	embryonic stem cell
40	chr3:156403600-156412000	Weak transcription	HUES6 Cell Line	embryonic stem cell
41	chr3:156403800-156407400	Weak transcription	Pancreas	Pancrea
42	chr3:156403800-156407400	Weak transcription	Right Ventricle	heart
43	chr3:156403800-156408400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
44	chr3:156403800-156408800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr3:156403800-156409600	Genic enhancers	HMEC	breast
46	chr3:156403800-156412200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr3:156403800-156413800	Weak transcription	Stomach Smooth Muscle	stomach
48	chr3:156404000-156406800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr3:156404000-156407000	Weak transcription	Cortex derived primary cultured neurospheres	brain
50	chr3:156404000-156407000	Enhancers	Duodenum Mucosa	Duodenum

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