Variant report

Variant	rs343991
Chromosome Location	chr3:156399742-156399743
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:156398277..156399955-chr3:156533630..156535549,2	MCF-7	breast:
2	chr3:156398881..156401137-chr3:156542792..156545641,2	MCF-7	breast:
3	chr3:156399372..156402148-chr3:156402188..156404792,4	MCF-7	breast:
4	chr3:156391507..156394071-chr3:156396999..156400389,4	MCF-7	breast:
5	chr3:156399612..156401929-chr3:156863576..156865457,2	K562	blood:
6	chr3:156398799..156400378-chr3:156543351..156545988,2	MCF-7	breast:
7	chr3:156397478..156399872-chr3:156533478..156536173,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000243926	Chromatin interaction
ENSG00000240875	Chromatin interaction
ENSG00000197980	Chromatin interaction
ENSG00000163659	Chromatin interaction

Extended variants
information (count: 92 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:91)

rs_ID	r²[population]
rs11710516	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1355280	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1397194	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1397195	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1510269	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1510270	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs168245	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs168295	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs171077	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs180746	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs180747	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs182935	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs182936	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs184677	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1858229	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs186928	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs193423	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2054881	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2129909	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2136691	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2136692	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs237245	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs237246	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2665390	0.95[ASN][1000 genomes]
rs343995	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs343996	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs343997	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs343998	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs344000	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs344001	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs344005	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs344006	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs344008	0.95[ASN][1000 genomes]
rs344009	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs344010	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs344011	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs344012	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs344013	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs344014	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs344015	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs344016	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs344017	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs344023	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs344029	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs344032	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs344047	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs344048	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs344049	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs344050	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs344052	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs344053	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs344054	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs344055	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs344058	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs344059	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs344060	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs344061	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs344062	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs344063	1.00[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs344064	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs344065	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs344066	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs344068	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs344069	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs344070	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs345987	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs419287	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs427384	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4279048	0.94[ASN][1000 genomes]
rs4429586	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4679784	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4680297	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4680298	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4680299	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs5012666	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6441089	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs6441092	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6441093	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6441094	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6441095	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6799457	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7640593	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs871232	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs871233	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs907063	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs931990	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs978108	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs978109	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9823112	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9833951	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9877043	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 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

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:156393600-156401800	Transcr. at gene 5' and 3'	Muscle Satellite Cultured Cells	--
2	chr3:156394000-156436000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr3:156394200-156412600	Weak transcription	Placenta	Placenta
4	chr3:156394400-156404800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
5	chr3:156394400-156411800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr3:156394600-156402200	Enhancers	Fetal Heart	heart
7	chr3:156394600-156402800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr3:156394800-156400600	Genic enhancers	K562	blood
9	chr3:156394800-156403000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr3:156395000-156400800	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr3:156395400-156400000	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr3:156395400-156400000	Genic enhancers	Liver	Liver
13	chr3:156395400-156401400	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr3:156395400-156402800	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
15	chr3:156395600-156399800	Transcr. at gene 5' and 3'	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr3:156395600-156399800	Strong transcription	Fetal Thymus	thymus
17	chr3:156395600-156400000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
18	chr3:156395600-156401800	Genic enhancers	HUVEC	blood vessel
19	chr3:156395600-156438600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr3:156395800-156400200	Genic enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr3:156395800-156400800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr3:156395800-156408600	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr3:156396200-156399800	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
24	chr3:156396200-156403600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr3:156396200-156407400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr3:156396400-156407400	Weak transcription	Esophagus	oesophagus
27	chr3:156396400-156407400	Weak transcription	Spleen	Spleen
28	chr3:156396400-156408800	Weak transcription	Colonic Mucosa	Colon
29	chr3:156396400-156413000	Weak transcription	Fetal Muscle Trunk	muscle
30	chr3:156396400-156414400	Weak transcription	Thymus	Thymus
31	chr3:156396400-156424800	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr3:156396600-156400600	Enhancers	Brain Angular Gyrus	brain
33	chr3:156396600-156441000	Weak transcription	Lung	lung
34	chr3:156397200-156399800	Transcr. at gene 5' and 3'	NHEK	skin
35	chr3:156397200-156400000	Transcr. at gene 5' and 3'	Breast Myoepithelial Primary Cells	Breast
36	chr3:156397200-156400200	Genic enhancers	Primary T cells from cord blood	blood
37	chr3:156397200-156400600	Enhancers	Fetal Intestine Small	intestine
38	chr3:156397200-156400600	Enhancers	Stomach Mucosa	stomach
39	chr3:156397400-156399800	Genic enhancers	Primary T cells fromperipheralblood	blood
40	chr3:156397600-156399800	Genic enhancers	Primary B cells from cord blood	blood
41	chr3:156397600-156400000	Enhancers	Sigmoid Colon	Sigmoid Colon
42	chr3:156397600-156403400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
43	chr3:156397600-156404000	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr3:156397800-156400000	Genic enhancers	HSMMtube	muscle
45	chr3:156397800-156413000	Weak transcription	H1 Cell Line	embryonic stem cell
46	chr3:156398000-156399800	Transcr. at gene 5' and 3'	A549	lung
47	chr3:156398000-156400200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr3:156398000-156400600	Enhancers	Skeletal Muscle Male	skeletal muscle
49	chr3:156398000-156400600	Enhancers	Small Intestine	intestine
50	chr3:156398200-156399800	Genic enhancers	Rectal Mucosa Donor 31	rectum

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