Variant report

Variant	rs73199734
Chromosome Location	chr13:52311956-52311957
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	RUNX3	chr13:52311730-52312147	GM12878	blood:	n/a	n/a
2	ZNF384	chr13:52311867-52312027	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:52158067..52160391-chr13:52310878..52313394,2	MCF-7	breast:
2	chr13:52024953..52028665-chr13:52311565..52316008,5	MCF-7	breast:

Variant related genes	Relation type
WDFY2	TF binding region
ENSG00000139668	Chromatin interaction
ENSG00000102786	Chromatin interaction
ENSG00000236778	Chromatin interaction
ENSG00000224892	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs1060562	1.00[ASN][1000 genomes]
rs12146894	1.00[ASN][1000 genomes]
rs12427748	0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1475195	1.00[AFR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17075907	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17532412	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17532524	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17532936	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17597215	1.00[AFR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17597531	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1885854	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2296028	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2296029	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2897944	0.99[ASN][1000 genomes]
rs3908968	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs41292776	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4555048	1.00[AFR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs483879	1.00[AFR][1000 genomes]
rs488261	1.00[AFR][1000 genomes]
rs60757273	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73199746	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9526783	1.00[AFR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9526786	1.00[AFR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9526788	1.00[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs9526793	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9526794	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9535714	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9535715	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9535717	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs9535722	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs9535734	0.92[ASN][1000 genomes]
rs9535735	0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9535737	1.00[AFR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9535738	1.00[AFR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9535739	1.00[AFR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9535741	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9535743	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535744	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535745	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535746	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9535747	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535748	0.99[ASN][1000 genomes]
rs9535749	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9535750	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9535751	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9535752	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9535753	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9535755	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9535756	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832612	chr13:52176983-52362525	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv530718	chr13:52291802-52832752	Enhancers ZNF genes & repeats Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
3	nsv933424	chr13:52293482-52507732	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
4	nsv455884	chr13:52302630-52405251	Enhancers Flanking Active TSS Strong transcription Genic enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
5	nsv561644	chr13:52302630-52405251	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:52288400-52322200	Weak transcription	K562	blood
2	chr13:52296400-52322200	Weak transcription	Fetal Heart	heart
3	chr13:52298000-52322200	Weak transcription	Fetal Brain Female	brain
4	chr13:52300400-52322200	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr13:52300600-52316000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr13:52300600-52321800	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr13:52302200-52314000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr13:52302400-52313000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr13:52302600-52313800	Weak transcription	Dnd41	blood
10	chr13:52302800-52313200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
11	chr13:52302800-52313200	Weak transcription	Primary T helper cells PMA-I stimulated	--
12	chr13:52303400-52315000	Weak transcription	Fetal Thymus	thymus
13	chr13:52303800-52313600	Weak transcription	Primary hematopoietic stem cells	blood
14	chr13:52304000-52320400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr13:52305000-52313000	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr13:52305000-52313200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr13:52305000-52313200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr13:52305000-52320400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr13:52305000-52338200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
20	chr13:52305200-52313200	Weak transcription	Placenta	Placenta
21	chr13:52305200-52320400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr13:52305400-52313800	Weak transcription	Fetal Muscle Trunk	muscle
23	chr13:52305400-52315000	Weak transcription	Fetal Stomach	stomach
24	chr13:52305400-52321600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
25	chr13:52305400-52321800	Weak transcription	Gastric	stomach
26	chr13:52305600-52314800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr13:52305800-52313000	Weak transcription	Primary T helper cells fromperipheralblood	blood
28	chr13:52305800-52322000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
29	chr13:52306000-52313000	Weak transcription	Duodenum Mucosa	Duodenum
30	chr13:52306000-52313200	Weak transcription	Fetal Lung	lung
31	chr13:52306000-52313200	Weak transcription	Pancreas	Pancrea
32	chr13:52306000-52314200	Weak transcription	NHLF	lung
33	chr13:52306000-52317800	Weak transcription	Small Intestine	intestine
34	chr13:52306000-52322200	Weak transcription	Left Ventricle	heart
35	chr13:52306000-52322200	Weak transcription	Right Ventricle	heart
36	chr13:52306200-52313000	Weak transcription	Colon Smooth Muscle	Colon
37	chr13:52306200-52313200	Weak transcription	Brain Germinal Matrix	brain
38	chr13:52306200-52321400	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr13:52306200-52339000	Weak transcription	Fetal Kidney	kidney
40	chr13:52306400-52312800	Weak transcription	Rectal Smooth Muscle	rectum
41	chr13:52306400-52313000	Weak transcription	NHDF-Ad	bronchial
42	chr13:52306400-52320400	Weak transcription	Aorta	Aorta
43	chr13:52306600-52313200	Weak transcription	Ovary	ovary
44	chr13:52307800-52312000	Strong transcription	Primary B cells from cord blood	blood
45	chr13:52307800-52313000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
46	chr13:52307800-52313200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
47	chr13:52308000-52313000	Weak transcription	Stomach Smooth Muscle	stomach
48	chr13:52308000-52313200	Weak transcription	H1 Cell Line	embryonic stem cell
49	chr13:52308000-52313200	Weak transcription	HUES6 Cell Line	embryonic stem cell
50	chr13:52308000-52313200	Weak transcription	Cortex derived primary cultured neurospheres	brain

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