Variant report

Variant	rs193197
Chromosome Location	chr3:156411732-156411733
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:156409314..156412375-chr3:156415973..156421497,5	K562	blood:
2	chr3:156390829..156393795-chr3:156408835..156412947,6	MCF-7	breast:
3	chr3:156410755..156413366-chr3:156533467..156535324,3	MCF-7	breast:
4	chr3:156409514..156412147-chr3:156532498..156534140,2	K562	blood:
5	chr3:156407951..156412215-chr3:156529722..156531947,3	MCF-7	breast:
6	chr3:156390628..156393358-chr3:156410469..156413701,3	K562	blood:
7	chr3:156407636..156412375-chr3:156415466..156420598,10	K562	blood:

Variant related genes	Relation type
ENSG00000240875	Chromatin interaction
ENSG00000243926	Chromatin interaction
ENSG00000163659	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs12497777	0.83[CHB][hapmap];0.88[CHD][hapmap];0.82[JPT][hapmap]
rs13314482	0.91[ASN][1000 genomes]
rs1367311	0.83[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs1469536	0.83[TSI][hapmap]
rs168247	0.88[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17380702	0.81[CHB][hapmap];0.88[CHD][hapmap]
rs17380954	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs184695	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];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs237250	0.86[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];0.91[LWK][hapmap];0.97[MKK][hapmap];0.82[YRI][hapmap];0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs343999	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs344003	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs344018	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs344027	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs344028	0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs344034	0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs344067	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs345985	0.96[CEU][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs345986	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs346003	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34901284	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs374341	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs386736	1.00[CHB][hapmap];0.88[CHD][hapmap];0.85[GIH][hapmap];0.82[JPT][hapmap]
rs62277393	0.91[ASN][1000 genomes]
rs62277394	0.91[ASN][1000 genomes]
rs7636965	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9289971	0.83[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap]
rs9882795	0.83[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs193197	Hs.54543	cis	multi-tissue	Pritchard

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	chr3:156396400-156413000	Weak transcription	Fetal Muscle Trunk	muscle
6	chr3:156396400-156414400	Weak transcription	Thymus	Thymus
7	chr3:156396400-156424800	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr3:156396600-156441000	Weak transcription	Lung	lung
9	chr3:156397800-156413000	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr3:156399200-156412400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr3:156399800-156411800	Enhancers	Brain Hippocampus Middle	brain
12	chr3:156399800-156413200	Weak transcription	Fetal Muscle Leg	muscle
13	chr3:156400000-156412200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
14	chr3:156403400-156421800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr3:156403600-156412000	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr3:156403800-156412200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr3:156403800-156413800	Weak transcription	Stomach Smooth Muscle	stomach
18	chr3:156404000-156411800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr3:156404000-156413000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr3:156404600-156411800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr3:156405200-156412200	Weak transcription	Primary neutrophils fromperipheralblood	blood
22	chr3:156405800-156413000	Weak transcription	Aorta	Aorta
23	chr3:156407000-156411800	Weak transcription	Primary B cells from peripheral blood	blood
24	chr3:156407800-156411800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr3:156407800-156411800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr3:156407800-156411800	Weak transcription	Psoas Muscle	Psoas
27	chr3:156407800-156412000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
28	chr3:156407800-156413200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
29	chr3:156407800-156415000	Weak transcription	Pancreas	Pancrea
30	chr3:156407800-156419600	Weak transcription	Esophagus	oesophagus
31	chr3:156407800-156422000	Weak transcription	Fetal Brain Female	brain
32	chr3:156407800-156423800	Weak transcription	Spleen	Spleen
33	chr3:156407800-156424000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr3:156407800-156428200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr3:156408800-156412400	Weak transcription	Fetal Kidney	kidney
36	chr3:156409000-156415000	Weak transcription	Right Ventricle	heart
37	chr3:156409000-156429800	Weak transcription	Gastric	stomach
38	chr3:156409200-156413800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
39	chr3:156409200-156422000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
40	chr3:156409200-156425400	Weak transcription	Colonic Mucosa	Colon
41	chr3:156409400-156412400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
42	chr3:156409400-156412600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr3:156409400-156413800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr3:156409400-156414200	Weak transcription	Fetal Heart	heart
45	chr3:156409400-156414200	Weak transcription	Ovary	ovary
46	chr3:156409400-156422200	Weak transcription	Skeletal Muscle Male	skeletal muscle
47	chr3:156409400-156425600	Weak transcription	Fetal Brain Male	brain
48	chr3:156409600-156412400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
49	chr3:156409600-156422400	Weak transcription	Fetal Stomach	stomach
50	chr3:156409800-156412200	Weak transcription	Colon Smooth Muscle	Colon

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