Variant report

Variant	rs11949203
Chromosome Location	chr5:179946059-179946060
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	chr5:179944903..179947278-chr5:179974741..179976598,2	MCF-7	breast:

Extended variants
information (count: 76 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs11249715	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11249723	0.90[CHB][hapmap];0.82[YRI][hapmap]
rs11249724	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11738060	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11740103	0.82[AMR][1000 genomes]
rs11740121	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11740213	1.00[CEU][hapmap];0.81[CHB][hapmap];0.87[CHD][hapmap];0.97[GIH][hapmap];0.82[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11740953	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11741030	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11742350	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11742375	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11743486	0.81[CHB][hapmap];0.80[CHD][hapmap];0.93[MEX][hapmap];0.84[TSI][hapmap];0.82[AMR][1000 genomes]
rs11744382	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11744428	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11744582	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11745477	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.90[YRI][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11745688	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11746130	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11747624	0.82[AMR][1000 genomes]
rs11748724	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11748792	1.00[CEU][hapmap];0.87[CHD][hapmap];0.94[GIH][hapmap];0.82[JPT][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11750477	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11750835	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11950075	0.84[ASN][1000 genomes]
rs11956078	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.91[YRI][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11957507	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11960298	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12109328	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12110046	1.00[CEU][hapmap];0.81[CHB][hapmap];0.87[CHD][hapmap];0.91[GIH][hapmap];0.82[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12719870	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13154631	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13156947	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13164771	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13166694	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13171439	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13171609	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13171921	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13174480	1.00[CHB][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13179742	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13181735	0.83[EUR][1000 genomes]
rs13182919	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13183429	1.00[CEU][hapmap];0.81[CHB][hapmap];0.82[JPT][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13187624	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17630549	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17698422	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2002074	0.80[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs34281336	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35076338	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35197594	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35490561	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35706747	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs56005965	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56039468	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60034484	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62405495	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62405496	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62405525	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62405531	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62405532	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62405547	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6898169	0.83[CHB][hapmap]
rs872365	0.81[CHB][hapmap];0.83[CHD][hapmap];0.82[GIH][hapmap];0.87[TSI][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs872366	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1023914	chr5:179649883-180040672	Weak transcription Enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv537983	chr5:179649883-180040672	Strong transcription ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv1030697	chr5:179710469-180686563	ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Genic enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	184 gene(s)	inside rSNPs	diseases
4	nsv1026417	chr5:179721376-180291360	Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
5	nsv1031836	chr5:179742033-180676122	Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	177 gene(s)	inside rSNPs	diseases
6	nsv537984	chr5:179742033-180676122	Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	177 gene(s)	inside rSNPs	diseases
7	nsv949199	chr5:179743553-180696889	Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	182 gene(s)	inside rSNPs	diseases
8	nsv1023537	chr5:179791679-179982822	Transcr. at gene 5' and 3' Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
9	nsv537985	chr5:179791679-179982822	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
10	nsv1019519	chr5:179866730-179959408	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
11	nsv830564	chr5:179867394-180010096	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
12	nsv519380	chr5:179942395-179951574	Flanking Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
13	esv1810959	chr5:179945112-179997861	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11949203	MXD3	cis	parietal	SCAN
rs11949203	BTNL3	cis	parietal	SCAN

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:179923600-179949800	Weak transcription	Gastric	stomach
2	chr5:179923600-179949800	Weak transcription	Psoas Muscle	Psoas
3	chr5:179923600-179957000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr5:179924000-179948000	Weak transcription	A549	lung
5	chr5:179924000-179949800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr5:179924200-179949200	Weak transcription	Pancreas	Pancrea
7	chr5:179924200-179949600	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr5:179924200-179950000	Weak transcription	Brain Angular Gyrus	brain
9	chr5:179924600-179949800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr5:179924600-179957000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr5:179925800-179949200	Weak transcription	Left Ventricle	heart
12	chr5:179926000-179947600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr5:179926800-179948600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr5:179927000-179947800	Weak transcription	NHEK	skin
15	chr5:179927000-179948000	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr5:179927000-179954400	Weak transcription	Hela-S3	cervix
17	chr5:179927400-179948200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
18	chr5:179927400-179948200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr5:179927400-179949200	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr5:179927400-179949200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr5:179927400-179949600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr5:179929000-179959200	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr5:179933800-179950000	Weak transcription	Colon Smooth Muscle	Colon
24	chr5:179933800-179959000	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr5:179934200-179948400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr5:179934200-179949600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
27	chr5:179934200-179956600	Weak transcription	Rectal Smooth Muscle	rectum
28	chr5:179935000-179951000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr5:179935200-179951400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
30	chr5:179935400-179948000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
31	chr5:179935400-179948200	Weak transcription	Primary T cells from cord blood	blood
32	chr5:179936800-179949200	Weak transcription	Thymus	Thymus
33	chr5:179936800-179949600	Weak transcription	Fetal Muscle Leg	muscle
34	chr5:179936800-179950000	Weak transcription	Fetal Stomach	stomach
35	chr5:179936800-179956200	Weak transcription	Fetal Muscle Trunk	muscle
36	chr5:179937400-179948200	Weak transcription	Brain Anterior Caudate	brain
37	chr5:179938800-179956600	Weak transcription	HSMM	muscle
38	chr5:179939200-179948600	Weak transcription	Fetal Thymus	thymus
39	chr5:179939400-179947800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr5:179939600-179946200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr5:179941800-179947800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr5:179942000-179951800	Weak transcription	Pancreatic Islets	Pancreatic Islet
43	chr5:179942000-179956400	Weak transcription	Brain Germinal Matrix	brain
44	chr5:179942000-179958800	Weak transcription	Esophagus	oesophagus
45	chr5:179942200-179949600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr5:179942400-179949600	Weak transcription	Spleen	Spleen
47	chr5:179942600-179948200	Weak transcription	GM12878-XiMat	blood
48	chr5:179942600-179950000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
49	chr5:179942600-179959000	Weak transcription	HepG2	liver
50	chr5:179942800-179948000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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