Variant report

Variant	rs12429350
Chromosome Location	chr13:50142463-50142464
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:50016440..50019751-chr13:50141127..50144444,4	MCF-7	breast:
2	chr13:50140129..50142488-chr13:50158778..50160378,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000136169	Chromatin interaction
ENSG00000102547	Chromatin interaction
ENSG00000136144	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs11148155	0.85[ASN][1000 genomes]
rs11619565	0.85[ASN][1000 genomes]
rs12429331	0.81[JPT][hapmap]
rs12430463	0.85[ASN][1000 genomes]
rs34449946	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs56076648	0.85[ASN][1000 genomes]
rs56856971	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs59549782	0.81[ASN][1000 genomes]
rs59934906	0.85[ASN][1000 genomes]
rs61959865	0.85[ASN][1000 genomes]
rs61959868	0.85[ASN][1000 genomes]
rs61959873	0.81[ASN][1000 genomes]
rs61961440	0.85[ASN][1000 genomes]
rs73192614	0.85[ASN][1000 genomes]
rs73192638	0.81[ASN][1000 genomes]
rs9316470	1.00[CHB][hapmap]
rs9568240	0.89[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1047311	chr13:49895019-50224227	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv916093	chr13:50050919-50290245	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv1036135	chr13:50071310-50183103	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv541770	chr13:50071310-50183103	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
5	nsv1054965	chr13:50102730-50251347	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
6	nsv541771	chr13:50102730-50251347	Enhancers Active TSS Genic enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
7	esv2763020	chr13:50105055-50192259	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
8	nsv900071	chr13:50107289-50286218	Weak transcription Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
9	nsv1052801	chr13:50116407-50144995	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
10	nsv561616	chr13:50120435-50190246	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
11	nsv949162	chr13:50120985-50195882	Flanking Active TSS Active TSS Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
12	nsv1046912	chr13:50122840-50189313	Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
13	nsv1043902	chr13:50122840-50189999	Strong transcription Flanking Active TSS Weak transcription Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
14	esv2761789	chr13:50122852-50185910	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
15	nsv455883	chr13:50124621-50185204	Flanking Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
16	nsv561617	chr13:50124621-50185204	Genic enhancers Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
17	nsv1043697	chr13:50129199-50249241	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:50075000-50143800	Weak transcription	Small Intestine	intestine
2	chr13:50088400-50151000	Weak transcription	Psoas Muscle	Psoas
3	chr13:50101600-50142800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr13:50104600-50143800	Weak transcription	Hela-S3	cervix
5	chr13:50108600-50158800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr13:50115400-50143200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr13:50122000-50158000	Weak transcription	Brain Germinal Matrix	brain
8	chr13:50124000-50158800	Weak transcription	Esophagus	oesophagus
9	chr13:50126400-50152400	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr13:50129000-50158800	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr13:50129800-50155200	Weak transcription	Spleen	Spleen
12	chr13:50130000-50144200	Weak transcription	GM12878-XiMat	blood
13	chr13:50130200-50143800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr13:50130400-50158800	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr13:50132400-50153600	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr13:50132400-50153800	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr13:50132400-50153800	Weak transcription	NH-A	brain
18	chr13:50133400-50154000	Weak transcription	Colon Smooth Muscle	Colon
19	chr13:50133800-50143800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
20	chr13:50134000-50143800	Weak transcription	Primary T helper cells PMA-I stimulated	--
21	chr13:50134200-50151000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr13:50134200-50158400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr13:50134200-50158400	Weak transcription	Fetal Brain Female	brain
24	chr13:50134400-50151000	Weak transcription	HSMMtube	muscle
25	chr13:50135000-50158600	Weak transcription	Rectal Smooth Muscle	rectum
26	chr13:50135200-50144200	Weak transcription	A549	lung
27	chr13:50135200-50144400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr13:50135200-50153400	Weak transcription	Gastric	stomach
29	chr13:50135200-50154000	Weak transcription	Placenta	Placenta
30	chr13:50135400-50143800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr13:50135400-50145600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr13:50135600-50143800	Weak transcription	NHEK	skin
33	chr13:50135600-50144000	Weak transcription	HUVEC	blood vessel
34	chr13:50135600-50144200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
35	chr13:50135600-50151000	Weak transcription	Skeletal Muscle Male	skeletal muscle
36	chr13:50135600-50151200	Weak transcription	Aorta	Aorta
37	chr13:50135600-50153800	Weak transcription	Duodenum Mucosa	Duodenum
38	chr13:50135600-50155200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr13:50135600-50158000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr13:50135600-50158400	Weak transcription	Osteobl	bone
41	chr13:50135800-50143800	Weak transcription	HMEC	breast
42	chr13:50135800-50153600	Weak transcription	HepG2	liver
43	chr13:50136200-50152200	Weak transcription	Primary B cells from cord blood	blood
44	chr13:50138200-50153400	Weak transcription	Thymus	Thymus
45	chr13:50138400-50153800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr13:50138600-50152200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr13:50138600-50157200	Weak transcription	Brain Cingulate Gyrus	brain
48	chr13:50138800-50146200	Weak transcription	Fetal Stomach	stomach
49	chr13:50139200-50153000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr13:50139200-50153000	Weak transcription	Cortex derived primary cultured neurospheres	brain

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