Variant report

Variant	rs13183429
Chromosome Location	chr5:180006832-180006833
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr5:180006778-180006918	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr5:180006284-180007049	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr5:180006800-180006873	MCF-7	breast:	n/a	n/a
4	POLR2A	chr5:180006752-180006880	GM12878	blood:	n/a	n/a
5	POLR2A	chr5:180006311-180006906	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr5:180006748-180006941	H1-hESC	embryonic stem cell:	n/a	n/a

Variant related genes	Relation type
ENSG00000263759	TF binding region

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs11249715	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11249724	0.96[CEU][hapmap];0.81[CHB][hapmap];0.82[JPT][hapmap];0.80[YRI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11738060	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11740121	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11740213	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11740953	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11741030	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11742350	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11742375	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11744382	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11744428	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11744582	0.85[EUR][1000 genomes]
rs11745477	1.00[CEU][hapmap];0.81[CHB][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11745688	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11748724	1.00[CEU][hapmap];0.81[CHB][hapmap];0.84[EUR][1000 genomes]
rs11748792	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11750477	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11949203	1.00[CEU][hapmap];0.81[CHB][hapmap];0.82[JPT][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11956078	1.00[CEU][hapmap];0.81[CHB][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11957507	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11960298	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12109328	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12110046	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12719870	0.83[EUR][1000 genomes]
rs13156947	0.84[EUR][1000 genomes]
rs13171439	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13171609	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13171921	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13174480	0.80[CEU][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13179742	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13181735	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13182919	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13187624	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17630549	0.84[EUR][1000 genomes]
rs17698422	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35076338	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs35197594	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35490561	0.83[EUR][1000 genomes]
rs56005965	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs56039468	0.85[EUR][1000 genomes]
rs60034484	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62405525	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62405531	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62405532	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62405547	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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	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
9	esv2762572	chr5:179996987-180183359	Bivalent Enhancer Strong transcription Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:179976200-180007200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr5:179993200-180007600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr5:179993400-180007200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr5:179993400-180008000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr5:179994200-180013800	Weak transcription	NHEK	skin
6	chr5:179995200-180009200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr5:180001200-180008600	Weak transcription	Right Ventricle	heart
8	chr5:180001200-180012400	Weak transcription	Fetal Intestine Small	intestine
9	chr5:180001200-180012400	Weak transcription	Lung	lung
10	chr5:180001400-180007000	Weak transcription	Aorta	Aorta
11	chr5:180001400-180007400	Weak transcription	Brain Anterior Caudate	brain
12	chr5:180001400-180007600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr5:180001400-180008000	Weak transcription	NHLF	lung
14	chr5:180001400-180008400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr5:180001400-180008600	Weak transcription	Thymus	Thymus
16	chr5:180001400-180009600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr5:180001400-180010000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr5:180001400-180010400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr5:180001600-180007800	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr5:180001600-180010800	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr5:180001800-180007800	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr5:180002600-180009200	Weak transcription	Fetal Brain Female	brain
23	chr5:180002800-180008400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr5:180003400-180007000	Weak transcription	Left Ventricle	heart
25	chr5:180003400-180007400	Weak transcription	Adipose Nuclei	Adipose
26	chr5:180003400-180008800	Weak transcription	Fetal Stomach	stomach
27	chr5:180003600-180007400	Weak transcription	Stomach Smooth Muscle	stomach
28	chr5:180003600-180008400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr5:180003600-180015600	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr5:180003800-180007400	Weak transcription	NHDF-Ad	bronchial
31	chr5:180003800-180007800	Weak transcription	Hela-S3	cervix
32	chr5:180003800-180008400	Weak transcription	Rectal Mucosa Donor 29	rectum
33	chr5:180003800-180009800	Weak transcription	HUVEC	blood vessel
34	chr5:180003800-180010000	Weak transcription	Osteobl	bone
35	chr5:180003800-180012200	Weak transcription	Primary T cells from cord blood	blood
36	chr5:180003800-180015000	Weak transcription	K562	blood
37	chr5:180004000-180008800	Weak transcription	Primary T cells fromperipheralblood	blood
38	chr5:180004400-180007000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
39	chr5:180004600-180007400	Weak transcription	H1 Cell Line	embryonic stem cell
40	chr5:180004600-180008000	Weak transcription	HMEC	breast
41	chr5:180004600-180009200	Weak transcription	Muscle Satellite Cultured Cells	--
42	chr5:180004800-180007000	Weak transcription	Fetal Lung	lung
43	chr5:180004800-180007000	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr5:180004800-180007200	Weak transcription	Psoas Muscle	Psoas
45	chr5:180004800-180007400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr5:180004800-180007400	Weak transcription	Skeletal Muscle Female	skeletal muscle
47	chr5:180004800-180007800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr5:180004800-180008200	Weak transcription	Fetal Muscle Leg	muscle
49	chr5:180004800-180008400	Weak transcription	Brain Germinal Matrix	brain
50	chr5:180004800-180011000	Weak transcription	NH-A	brain

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