Variant report

Variant	rs1936401
Chromosome Location	chr9:96031262-96031263
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:95894565..95896559-chr9:96029848..96032324,3	MCF-7	breast:
2	chr9:96031002..96033889-chr9:96054766..96056990,2	MCF-7	breast:
3	chr9:96029425..96032185-chr9:96033785..96035913,2	K562	blood:

Variant related genes	Relation type
ENSG00000131669	Chromatin interaction
ENSG00000165238	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10733747	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10761206	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10761208	1.00[EUR][1000 genomes]
rs10821104	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1111776	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12683662	0.94[EUR][1000 genomes]
rs12684392	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12684553	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1343631	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1891970	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1931365	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1931366	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1931367	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1931368	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2169756	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4147136	0.97[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4743908	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4743909	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4744209	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4744210	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4744214	0.97[EUR][1000 genomes]
rs6479470	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6479472	1.00[EUR][1000 genomes]
rs6479473	0.85[EUR][1000 genomes]
rs7020940	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7021187	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7042028	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7042492	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7856268	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7866298	1.00[EUR][1000 genomes]
rs7872608	0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv893576	chr9:95789960-96158277	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv893580	chr9:95855100-96099377	Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv430082	chr9:95905745-96095045	Genic enhancers Enhancers Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv893582	chr9:95963114-96116937	Bivalent Enhancer Bivalent/Poised TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv893583	chr9:95996573-96091688	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv893584	chr9:96002983-96116937	Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS Strong transcription Flanking Active 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	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:96005400-96033800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr9:96006200-96043800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr9:96011200-96032800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr9:96011200-96033400	Weak transcription	A549	lung
5	chr9:96012800-96032600	Weak transcription	Fetal Brain Male	brain
6	chr9:96013000-96031400	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr9:96014000-96033800	Strong transcription	Stomach Smooth Muscle	stomach
8	chr9:96014400-96032800	Strong transcription	Fetal Brain Female	brain
9	chr9:96017400-96033200	Weak transcription	Brain Substantia Nigra	brain
10	chr9:96018400-96033200	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr9:96024200-96033600	Strong transcription	Fetal Stomach	stomach
12	chr9:96024400-96031600	Strong transcription	HepG2	liver
13	chr9:96025400-96035600	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr9:96025600-96041200	Weak transcription	Psoas Muscle	Psoas
15	chr9:96026200-96033200	Strong transcription	Brain Germinal Matrix	brain
16	chr9:96026400-96031400	Strong transcription	Rectal Smooth Muscle	rectum
17	chr9:96027000-96036800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr9:96027200-96035200	Weak transcription	Brain Hippocampus Middle	brain
19	chr9:96027200-96051200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr9:96027200-96056000	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr9:96027200-96061000	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr9:96027600-96032800	Weak transcription	Placenta	Placenta
23	chr9:96028600-96033000	Weak transcription	Small Intestine	intestine
24	chr9:96028600-96036200	Weak transcription	Fetal Heart	heart
25	chr9:96029000-96031400	Genic enhancers	Pancreas	Pancrea
26	chr9:96029200-96032200	Genic enhancers	Duodenum Mucosa	Duodenum
27	chr9:96029200-96033600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr9:96029200-96033600	Enhancers	Dnd41	blood
29	chr9:96029200-96033800	Strong transcription	Skeletal Muscle Male	skeletal muscle
30	chr9:96029400-96031600	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr9:96029600-96031600	Enhancers	Esophagus	oesophagus
32	chr9:96029600-96031800	Strong transcription	Right Ventricle	heart
33	chr9:96029600-96032000	Genic enhancers	Rectal Mucosa Donor 31	rectum
34	chr9:96029800-96031400	Genic enhancers	Colonic Mucosa	Colon
35	chr9:96029800-96032600	Strong transcription	Brain Cingulate Gyrus	brain
36	chr9:96029800-96033400	Strong transcription	H9 Cell Line	embryonic stem cell
37	chr9:96029800-96033600	Strong transcription	HUES6 Cell Line	embryonic stem cell
38	chr9:96030000-96033000	Strong transcription	Skeletal Muscle Female	skeletal muscle
39	chr9:96030000-96033600	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr9:96030200-96031400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
41	chr9:96030200-96031400	Enhancers	Gastric	stomach
42	chr9:96030200-96032200	Genic enhancers	Fetal Intestine Small	intestine
43	chr9:96030200-96033000	Strong transcription	Brain Angular Gyrus	brain
44	chr9:96030200-96033600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
45	chr9:96030200-96033600	Strong transcription	Left Ventricle	heart
46	chr9:96030200-96033800	Strong transcription	Colon Smooth Muscle	Colon
47	chr9:96030400-96031400	Genic enhancers	Sigmoid Colon	Sigmoid Colon
48	chr9:96030400-96031600	Genic enhancers	Fetal Intestine Large	intestine
49	chr9:96030400-96033400	Strong transcription	Fetal Muscle Leg	muscle
50	chr9:96030400-96033400	Enhancers	Stomach Mucosa	stomach

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