Variant report

Variant	rs12341303
Chromosome Location	chr9:96003435-96003436
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:95982340..95984342-chr9:96001174..96003996,2	K562	blood:
2	chr9:95996764..96000673-chr9:96002959..96005853,3	MCF-7	breast:
3	chr9:95856433..95858666-chr9:96002592..96004391,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000165238	Chromatin interaction
ENSG00000165233	Chromatin interaction
ENSG00000223446	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10761203	0.96[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10821080	1.00[CEU][hapmap];0.95[MEX][hapmap]
rs10821086	0.92[CEU][hapmap];0.87[MEX][hapmap]
rs10821088	1.00[CEU][hapmap]
rs10821095	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10821098	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10992698	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10992702	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12336667	1.00[CEU][hapmap];0.87[MEX][hapmap];0.84[TSI][hapmap]
rs12684394	0.93[ASN][1000 genomes]
rs1317698	0.96[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13292831	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13293217	0.85[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap];0.84[ASN][1000 genomes]
rs1544229	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs16936753	0.82[JPT][hapmap]
rs2040093	0.92[CEU][hapmap]
rs2040094	0.92[CEU][hapmap]
rs2086103	0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2306183	0.96[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2398820	0.81[GIH][hapmap]
rs2398822	0.99[ASN][1000 genomes]
rs35795732	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3763634	0.94[CHB][hapmap];0.94[ASN][1000 genomes]
rs3763635	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3793546	0.90[ASN][1000 genomes]
rs4743911	0.92[CEU][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4744192	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4744195	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4744201	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4744203	0.81[ASN][1000 genomes]
rs4744206	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4744212	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4744215	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7846729	0.85[CEU][hapmap]
rs7857039	0.91[CEU][hapmap]
rs7857937	0.92[CEU][hapmap];0.87[MEX][hapmap]
rs7868971	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs944993	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv526296	chr9:95708192-96030392	Enhancers Bivalent/Poised TSS Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	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
6	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
7	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:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:95986200-96006800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr9:95987400-96005200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr9:95988200-96006800	Weak transcription	Esophagus	oesophagus
4	chr9:95993600-96005000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr9:95995200-96026400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr9:95995600-96030600	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr9:95996400-96004400	Strong transcription	Fetal Brain Female	brain
8	chr9:95996400-96011200	Strong transcription	Stomach Smooth Muscle	stomach
9	chr9:95997000-96012400	Weak transcription	Fetal Kidney	kidney
10	chr9:95997600-96007000	Weak transcription	Psoas Muscle	Psoas
11	chr9:95997600-96012400	Weak transcription	Fetal Brain Male	brain
12	chr9:95998200-96005800	Weak transcription	Rectal Smooth Muscle	rectum
13	chr9:95998200-96007200	Weak transcription	Brain Angular Gyrus	brain
14	chr9:95998400-96006400	Strong transcription	Fetal Intestine Large	intestine
15	chr9:95998400-96007000	Weak transcription	Brain Hippocampus Middle	brain
16	chr9:95998400-96007000	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr9:95998800-96006600	Strong transcription	Fetal Intestine Small	intestine
18	chr9:95999200-96006400	Strong transcription	Duodenum Mucosa	Duodenum
19	chr9:95999200-96006800	Weak transcription	Stomach Mucosa	stomach
20	chr9:96000400-96004200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr9:96000600-96004000	Strong transcription	Gastric	stomach
22	chr9:96000600-96010400	Weak transcription	Fetal Thymus	thymus
23	chr9:96001000-96003800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
24	chr9:96001200-96004600	Genic enhancers	Pancreas	Pancrea
25	chr9:96001200-96006000	Strong transcription	Rectal Mucosa Donor 31	rectum
26	chr9:96001400-96006200	Weak transcription	Colon Smooth Muscle	Colon
27	chr9:96001800-96003600	Genic enhancers	HepG2	liver
28	chr9:96001800-96018800	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr9:96002000-96005800	Weak transcription	Placenta	Placenta
30	chr9:96002200-96003600	ZNF genes & repeats	Fetal Stomach	stomach
31	chr9:96002200-96004400	Enhancers	Breast Myoepithelial Primary Cells	Breast
32	chr9:96002400-96004200	Weak transcription	HUES48 Cell Line	embryonic stem cell
33	chr9:96002400-96009400	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr9:96002400-96010600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
35	chr9:96002600-96004000	Weak transcription	Spleen	Spleen
36	chr9:96002600-96004200	Weak transcription	Colonic Mucosa	Colon
37	chr9:96002600-96004600	Weak transcription	Skeletal Muscle Male	skeletal muscle
38	chr9:96002600-96005200	Weak transcription	H1 Cell Line	embryonic stem cell
39	chr9:96002600-96016400	Weak transcription	Brain Cingulate Gyrus	brain
40	chr9:96002800-96003600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr9:96002800-96005000	Enhancers	Fetal Muscle Leg	muscle
42	chr9:96002800-96005200	Weak transcription	HUES6 Cell Line	embryonic stem cell
43	chr9:96002800-96007000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr9:96003000-96005000	Weak transcription	Brain Anterior Caudate	brain
45	chr9:96003000-96007600	Weak transcription	Sigmoid Colon	Sigmoid Colon
46	chr9:96003200-96003600	Genic enhancers	Brain Germinal Matrix	brain
47	chr9:96003200-96003600	Enhancers	Fetal Heart	heart
48	chr9:96003200-96003800	Genic enhancers	Skeletal Muscle Female	skeletal muscle
49	chr9:96003200-96004200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr9:96003200-96007000	Bivalent Enhancer	Fetal Muscle Trunk	muscle

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