Variant report

Variant	rs12802399
Chromosome Location	chr11:85756825-85756826
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:85755861..85758384-chr11:85778861..85780812,2	MCF-7	breast:
2	chr11:85755134..85758081-chr11:85773891..85777241,3	K562	blood:
3	chr11:85755599..85757870-chr11:85777185..85779857,2	K562	blood:

Variant related genes	Relation type
ENSG00000073921	Chromatin interaction

Extended variants
information (count: 80 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10501599	1.00[CHB][hapmap]
rs10501601	1.00[CHB][hapmap]
rs10501602	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11234465	1.00[CHB][hapmap]
rs11234467	1.00[CHB][hapmap]
rs11821654	1.00[CEU][hapmap]
rs12274739	1.00[CHB][hapmap]
rs12274987	0.91[CEU][hapmap]
rs12283410	0.91[CEU][hapmap]
rs12286312	1.00[CHB][hapmap]
rs12787412	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12787418	0.81[AMR][1000 genomes]
rs12787556	0.81[AMR][1000 genomes]
rs12788654	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12790526	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12790645	0.91[CEU][hapmap]
rs12791520	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12794211	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12795381	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12795833	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12798898	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12804751	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12804833	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12805520	1.00[CEU][hapmap]
rs1445508	1.00[CHB][hapmap]
rs17148574	1.00[CHB][hapmap]
rs17148585	1.00[CHB][hapmap]
rs17148704	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17745024	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17745409	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs17817402	1.00[CHB][hapmap]
rs17817444	1.00[CHB][hapmap]
rs17817600	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17817648	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17817931	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17817992	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28365806	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3213934	0.91[CEU][hapmap]
rs34003294	0.83[AMR][1000 genomes]
rs34223518	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34332755	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34584483	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34675784	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34700169	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34766621	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34874199	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34959028	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35206999	0.95[ASN][1000 genomes]
rs35220752	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35585561	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35866111	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35992035	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs41489645	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs55932210	0.81[AMR][1000 genomes]
rs56094546	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56191920	0.81[AMR][1000 genomes]
rs66494408	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs66802900	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs67282763	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs67682051	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs67719619	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7107455	0.91[CEU][hapmap]
rs7118279	1.00[CEU][hapmap]
rs71465611	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs725459	1.00[CHB][hapmap]
rs7926846	1.00[CHB][hapmap]
rs7934759	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1035489	chr11:85502953-85778229	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv1053808	chr11:85588919-85757693	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
3	nsv468769	chr11:85683554-85757589	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv555641	chr11:85683554-85757589	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv898054	chr11:85683554-85772636	Enhancers Genic enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv468771	chr11:85688209-85757589	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
7	nsv468773	chr11:85688209-85757589	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv555643	chr11:85688209-85757589	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	nsv468774	chr11:85688209-85775059	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
10	nsv555644	chr11:85688209-85775059	Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
11	esv1829985	chr11:85740319-85789350	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
12	nsv1050948	chr11:85756325-85968665	Active TSS Genic enhancers Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
13	nsv541117	chr11:85756325-85968665	Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:85742800-85758400	Weak transcription	Fetal Intestine Large	intestine
2	chr11:85746600-85762800	Weak transcription	Stomach Mucosa	stomach
3	chr11:85750200-85758200	Weak transcription	Fetal Intestine Small	intestine
4	chr11:85750600-85758800	Weak transcription	Fetal Muscle Trunk	muscle
5	chr11:85751400-85761800	Enhancers	Liver	Liver
6	chr11:85751600-85757600	Enhancers	Primary neutrophils fromperipheralblood	blood
7	chr11:85751600-85758200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
8	chr11:85751800-85760600	Enhancers	Primary T cells from cord blood	blood
9	chr11:85751800-85761200	Enhancers	Primary monocytes fromperipheralblood	blood
10	chr11:85752400-85758000	Enhancers	Hela-S3	cervix
11	chr11:85752400-85759000	Enhancers	Primary T helper cells PMA-I stimulated	--
12	chr11:85752400-85760600	Enhancers	Primary T killer memory cells from peripheral blood	blood
13	chr11:85752400-85768400	Enhancers	Primary T helper cells fromperipheralblood	blood
14	chr11:85752800-85758400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
15	chr11:85752800-85768200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
16	chr11:85752800-85776400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
17	chr11:85753000-85763000	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr11:85753200-85758600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr11:85753200-85759000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr11:85753200-85762200	Enhancers	Adipose Nuclei	Adipose
21	chr11:85753200-85764600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr11:85753200-85768000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
23	chr11:85753400-85758000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr11:85753800-85759400	Enhancers	Breast Myoepithelial Primary Cells	Breast
25	chr11:85754000-85764000	Weak transcription	Rectal Mucosa Donor 29	rectum
26	chr11:85754200-85757200	Weak transcription	Small Intestine	intestine
27	chr11:85754200-85757800	Weak transcription	Primary hematopoietic stem cells	blood
28	chr11:85754200-85764000	Weak transcription	HUES6 Cell Line	embryonic stem cell
29	chr11:85754200-85765200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr11:85754400-85757000	Weak transcription	NHEK	skin
31	chr11:85754400-85757200	Weak transcription	Rectal Smooth Muscle	rectum
32	chr11:85754400-85757400	Enhancers	Monocytes-CD14+_RO01746	blood
33	chr11:85754400-85758400	Weak transcription	Fetal Kidney	kidney
34	chr11:85754400-85759800	Weak transcription	Rectal Mucosa Donor 31	rectum
35	chr11:85754400-85763000	Weak transcription	HUVEC	blood vessel
36	chr11:85754400-85768200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
37	chr11:85754600-85762600	Enhancers	Primary T helper naive cells from peripheral blood	blood
38	chr11:85755200-85758200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
39	chr11:85755200-85758400	Enhancers	Brain Angular Gyrus	brain
40	chr11:85755200-85761200	Enhancers	Primary T cells fromperipheralblood	blood
41	chr11:85755200-85762800	Weak transcription	Fetal Lung	lung
42	chr11:85755400-85758800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
43	chr11:85755600-85761400	Weak transcription	Duodenum Mucosa	Duodenum
44	chr11:85755800-85757000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr11:85755800-85757600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr11:85755800-85757800	Weak transcription	Stomach Smooth Muscle	stomach
47	chr11:85755800-85758200	Weak transcription	Fetal Thymus	thymus
48	chr11:85755800-85758200	Weak transcription	A549	lung
49	chr11:85755800-85759200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr11:85755800-85759400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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