Variant report

Variant	rs13192365
Chromosome Location	chr6:25993968-25993969
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:25726594..25729863-chr6:25991893..25994558,4	K562	blood:
2	chr6:25990980..25994781-chr6:26019644..26023390,9	MCF-7	breast:
3	chr6:25867711..25870516-chr6:25992020..25994438,2	K562	blood:
4	chr6:25961783..25964529-chr6:25992813..25995946,4	MCF-7	breast:
5	chr6:25992154..25994849-chr6:27113422..27115157,2	K562	blood:
6	chr6:25992957..25995819-chr6:25996424..25999435,3	MCF-7	breast:
7	chr6:25992191..25994174-chr6:26011944..26014564,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000272558	Chromatin interaction
ENSG00000197903	Chromatin interaction
ENSG00000196176	Chromatin interaction
ENSG00000184825	Chromatin interaction
ENSG00000164508	Chromatin interaction
ENSG00000198366	Chromatin interaction
ENSG00000272810	Chromatin interaction
ENSG00000124564	Chromatin interaction
ENSG00000112343	Chromatin interaction
ENSG00000146047	Chromatin interaction

Extended variants
information (count: 98 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs1045537	0.92[CEU][hapmap];1.00[CHB][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10484433	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10484435	0.91[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13191445	0.83[CEU][hapmap]
rs13191776	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13192713	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13193424	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13195279	0.83[CEU][hapmap];1.00[CHB][hapmap];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13195692	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13196552	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13197334	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13198474	0.83[CEU][hapmap]
rs13200797	1.00[CEU][hapmap];1.00[CHB][hapmap];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13200888	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13201341	0.83[CEU][hapmap]
rs13201821	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13202371	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13202688	0.83[CEU][hapmap]
rs13203673	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13206443	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13206501	0.92[CEU][hapmap];1.00[CHB][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13207673	0.83[CEU][hapmap];1.00[CHB][hapmap];0.84[EUR][1000 genomes]
rs13210399	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13211947	0.83[CEU][hapmap]
rs13212652	0.83[EUR][1000 genomes]
rs13214280	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13216785	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13220395	0.91[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13220488	0.84[EUR][1000 genomes]
rs16891235	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16891261	0.90[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16891264	0.91[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16891315	0.92[CEU][hapmap];1.00[CHB][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16891334	0.92[CEU][hapmap];1.00[CHB][hapmap];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17586553	0.83[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17586784	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17587226	0.91[CEU][hapmap];0.81[EUR][1000 genomes]
rs17587597	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2051539	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28360595	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34027471	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs34116162	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34233736	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34391493	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs34791189	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34804024	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs35069699	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35116528	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35169013	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35249036	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35335639	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35367169	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35378061	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs35402046	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35484309	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35528636	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35778245	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35825164	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35902160	1.00[ASN][1000 genomes]
rs36012762	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3734523	0.83[CEU][hapmap];1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs3734528	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3752417	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs56195001	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56294283	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60512607	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66790453	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67296946	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67491322	0.81[EUR][1000 genomes]
rs67844427	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs68149500	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6931120	0.81[ASN][1000 genomes]
rs6940007	0.83[CEU][hapmap];1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs71557315	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs71557316	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72832596	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72834617	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72834623	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7748167	0.83[CEU][hapmap];1.00[CHB][hapmap]
rs7749414	1.00[ASN][1000 genomes]
rs9295675	0.83[CEU][hapmap];1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs9461222	0.83[CEU][hapmap];1.00[CHB][hapmap]
rs9461223	0.81[ASN][1000 genomes]
rs9467635	0.83[CEU][hapmap]
rs9467684	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	nsv1029920	chr6:25638507-26585842	Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1215 gene(s)	inside rSNPs	diseases
2	nsv538162	chr6:25638507-26585842	Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1215 gene(s)	inside rSNPs	diseases
3	nsv1030351	chr6:25813178-26352046	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1189 gene(s)	inside rSNPs	diseases
4	nsv1023453	chr6:25853830-26528250	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1201 gene(s)	inside rSNPs	diseases
5	nsv1025237	chr6:25874326-26280867	Flanking Active TSS Active TSS Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1166 gene(s)	inside rSNPs	diseases
6	nsv538163	chr6:25874326-26280867	Enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1166 gene(s)	inside rSNPs	diseases
7	nsv432857	chr6:25957109-26072445	Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	451 gene(s)	inside rSNPs	diseases
8	nsv1015627	chr6:25973495-26100483	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	447 gene(s)	inside rSNPs	diseases
9	nsv538164	chr6:25973495-26100483	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	447 gene(s)	inside rSNPs	diseases
10	nsv1028456	chr6:25984457-26174993	Active TSS Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	873 gene(s)	inside rSNPs	diseases
11	nsv538165	chr6:25984457-26174993	Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	873 gene(s)	inside rSNPs	diseases
12	nsv428137	chr6:25987413-26351920	Enhancers Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1181 gene(s)	inside rSNPs	diseases
13	nsv916992	chr6:25991630-26280921	Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1159 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13192365	BTN3A2	Cis_1M	lymphoblastoid	RTeQTL
rs13192365	BTN3A2///BTN3A3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25991600-25994000	Active TSS	Rectal Mucosa Donor 29	rectum
2	chr6:25991800-25994000	Active TSS	Hela-S3	cervix
3	chr6:25991800-25994200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr6:25991800-25994200	Active TSS	Stomach Smooth Muscle	stomach
5	chr6:25992000-25994000	Active TSS	HUES48 Cell Line	embryonic stem cell
6	chr6:25992000-25994000	Active TSS	HUES64 Cell Line	embryonic stem cell
7	chr6:25992000-25994000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr6:25992000-25994000	Active TSS	Fetal Lung	lung
9	chr6:25992000-25994000	Active TSS	Right Atrium	heart
10	chr6:25992000-25994000	Active TSS	Right Ventricle	heart
11	chr6:25992000-25994200	Active TSS	iPS-15b Cell Line	embryonic stem cell
12	chr6:25992000-25994200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr6:25992000-25994200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr6:25992000-25994200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
15	chr6:25992000-25994200	Active TSS	Fetal Intestine Large	intestine
16	chr6:25992000-25994200	Active TSS	Ovary	ovary
17	chr6:25992000-25994200	Active TSS	A549	lung
18	chr6:25992000-25994400	Active TSS	Brain Germinal Matrix	brain
19	chr6:25992000-25994600	Active TSS	ES-I3 Cell Line	embryonic stem cell
20	chr6:25992200-25994200	Active TSS	Duodenum Mucosa	Duodenum
21	chr6:25992200-25994200	Active TSS	Skeletal Muscle Female	skeletal muscle
22	chr6:25992400-25994000	Active TSS	Rectal Mucosa Donor 31	rectum
23	chr6:25992400-25994000	Active TSS	Skeletal Muscle Male	skeletal muscle
24	chr6:25992400-25994200	Active TSS	GM12878-XiMat	blood
25	chr6:25992600-25994000	Active TSS	HUES6 Cell Line	embryonic stem cell
26	chr6:25992600-25994000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr6:25992600-25994000	Active TSS	Rectal Smooth Muscle	rectum
28	chr6:25992600-25994000	Active TSS	NHDF-Ad	bronchial
29	chr6:25992600-25994400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr6:25992800-25994000	Active TSS	Muscle Satellite Cultured Cells	--
31	chr6:25993200-25994000	Flanking Active TSS	Adipose Nuclei	Adipose
32	chr6:25993200-25994200	Weak transcription	Spleen	Spleen
33	chr6:25993400-25994000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
34	chr6:25993400-25994000	Flanking Active TSS	HUVEC	blood vessel
35	chr6:25993400-25994200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
36	chr6:25993400-25994200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
37	chr6:25993400-25994200	Weak transcription	Brain Cingulate Gyrus	brain
38	chr6:25993400-25994400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr6:25993400-25994400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr6:25993400-25994400	Flanking Active TSS	Dnd41	blood
41	chr6:25993400-25994600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr6:25993400-25997800	Weak transcription	Sigmoid Colon	Sigmoid Colon
43	chr6:25993400-25998000	Weak transcription	Lung	lung
44	chr6:25993400-25998400	Weak transcription	Gastric	stomach
45	chr6:25993400-26001000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr6:25993400-26001200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr6:25993400-26004200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
48	chr6:25993400-26007400	Weak transcription	Small Intestine	intestine
49	chr6:25993600-25994000	Enhancers	Primary neutrophils fromperipheralblood	blood
50	chr6:25993600-25994000	Enhancers	Primary B cells from cord blood	blood

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