Variant report

Variant	rs6912853
Chromosome Location	chr6:26401438-26401439
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RFX5	chr6:26400501-26404941	SK-N-SH	brain:	n/a	chr6:26402430-26402439 chr6:26402427-26402442 chr6:26402461-26402470 chr6:26402437-26402445
2	RFX5	chr6:26400836-26403269	IMR90	lung:	n/a	chr6:26402430-26402439 chr6:26402427-26402442 chr6:26402461-26402470 chr6:26402437-26402445

No.	Distal block	Cell Line	Cell type
1	chr6:26399787..26402548-chr6:26520304..26522588,2	K562	blood:
2	chr6:26400774..26405587-chr6:26406042..26409897,8	K562	blood:
3	chr6:26400255..26403237-chr6:26521906..26524697,3	K562	blood:

Variant related genes	Relation type
BTN3A1	TF binding region
ENSG00000026950	Chromatin interaction
ENSG00000228223	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10456330	1.00[CHB][hapmap];0.93[ASN][1000 genomes]
rs10484440	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs10946822	0.95[ASN][1000 genomes]
rs12189841	1.00[CHB][hapmap]
rs12189870	1.00[CEU][hapmap];0.88[TSI][hapmap];0.91[EUR][1000 genomes]
rs12195971	1.00[CHB][hapmap]
rs12199239	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs12200782	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs12201802	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs12207181	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs12208220	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs12208390	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs12211201	1.00[CHB][hapmap]
rs12213722	1.00[CHB][hapmap]
rs2237233	0.91[EUR][1000 genomes]
rs3757142	1.00[CEU][hapmap];0.88[TSI][hapmap];0.91[EUR][1000 genomes]
rs3757144	0.90[EUR][1000 genomes]
rs3757146	1.00[CEU][hapmap];0.88[TSI][hapmap];0.91[EUR][1000 genomes]
rs3757148	1.00[CEU][hapmap];0.88[TSI][hapmap];0.91[EUR][1000 genomes]
rs3757149	0.82[CHD][hapmap]
rs3927423	0.82[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs41266837	0.95[ASN][1000 genomes]
rs41267923	0.90[ASN][1000 genomes]
rs4490658	0.91[EUR][1000 genomes]
rs59438701	0.95[ASN][1000 genomes]
rs72843734	0.90[ASN][1000 genomes]
rs7756881	1.00[CEU][hapmap];0.88[TSI][hapmap];0.91[EUR][1000 genomes]
rs7757048	1.00[CEU][hapmap];0.88[TSI][hapmap];0.91[EUR][1000 genomes]
rs7775720	1.00[CEU][hapmap];0.88[TSI][hapmap];0.91[EUR][1000 genomes]
rs9461246	0.84[CHD][hapmap]
rs9461249	0.84[CHD][hapmap]
rs9461250	0.91[EUR][1000 genomes]
rs9467730	0.89[EUR][1000 genomes]
rs9467731	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs9467733	0.88[EUR][1000 genomes]
rs9467734	0.88[EUR][1000 genomes]
rs9467735	0.89[EUR][1000 genomes]
rs9467738	0.91[EUR][1000 genomes]
rs9467739	0.91[EUR][1000 genomes]
rs9467740	0.81[EUR][1000 genomes]
rs9467741	0.84[CHD][hapmap]
rs9467742	0.91[EUR][1000 genomes]
rs9467743	0.91[EUR][1000 genomes]
rs9467745	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs9467746	0.91[EUR][1000 genomes]
rs9467747	0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:20 , 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	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
4	nsv482729	chr6:26291011-26470898	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer 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 miRNA target site	45 gene(s)	inside rSNPs	diseases
5	nsv482836	chr6:26352883-26520964	Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
6	nsv883491	chr6:26367689-26410800	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
7	nsv883492	chr6:26367689-26436592	Genic enhancers Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
8	nsv883493	chr6:26367689-26442786	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats 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	27 gene(s)	inside rSNPs	diseases
9	nsv883494	chr6:26367833-26442786	Enhancers Genic enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS ZNF genes & repeats 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	27 gene(s)	inside rSNPs	diseases
10	nsv883495	chr6:26367833-26443853	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
11	esv3334611	chr6:26367893-26443308	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
12	nsv482407	chr6:26369320-26550148	Active TSS Strong transcription Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
13	nsv883496	chr6:26369549-26413088	Weak transcription Genic enhancers Enhancers Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
14	nsv883497	chr6:26369549-26442786	Flanking Active TSS Active TSS Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
15	nsv883498	chr6:26369549-26443853	Strong transcription Flanking Active TSS Weak transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats 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	27 gene(s)	inside rSNPs	diseases
16	nsv1030863	chr6:26371006-26405990	Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
17	nsv883499	chr6:26377591-26454454	Enhancers Flanking Active TSS Genic enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats 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	28 gene(s)	inside rSNPs	diseases
18	esv3427999	chr6:26378373-26453532	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers 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 lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
19	nsv462664	chr6:26379537-26451553	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
20	nsv601184	chr6:26379537-26451553	Active TSS Genic enhancers Weak transcription Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs6912853	HMGN4	cis	parietal	SCAN
rs6912853	BTN3A1	cis	cerebellum	SCAN
rs6912853	BTN3A2	cis	parietal	SCAN
rs6912853	BTN3A2	cis	cerebellum	SCAN
rs6912853	BTN3A2	cis	multi-tissue	Pritchard
rs6912853	UTY	trans	lymphoblastoid	seeQTL
rs6912853	SCGN	cis	cerebellum	SCAN
rs6912853	ZNF192	cis	parietal	SCAN
rs6912853	BTN3A3	cis	cerebellum	SCAN

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:26384200-26402000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr6:26384200-26402400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr6:26384200-26402400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr6:26384200-26402400	Weak transcription	Pancreas	Pancrea
5	chr6:26384400-26402000	Weak transcription	Fetal Kidney	kidney
6	chr6:26384600-26401800	Weak transcription	Fetal Lung	lung
7	chr6:26385200-26401800	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr6:26385800-26402000	Weak transcription	Colonic Mucosa	Colon
9	chr6:26388200-26402000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr6:26388800-26401800	Weak transcription	Placenta	Placenta
11	chr6:26391200-26401600	Weak transcription	Aorta	Aorta
12	chr6:26391200-26401600	Weak transcription	Liver	Liver
13	chr6:26391200-26401800	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr6:26391200-26402000	Weak transcription	Right Ventricle	heart
15	chr6:26391200-26402400	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr6:26391800-26402000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr6:26392200-26402000	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr6:26392200-26402000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
19	chr6:26392200-26402000	Weak transcription	Left Ventricle	heart
20	chr6:26392400-26401600	Weak transcription	Brain Anterior Caudate	brain
21	chr6:26392400-26401600	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr6:26392400-26401800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr6:26392600-26401600	Weak transcription	Colon Smooth Muscle	Colon
24	chr6:26392800-26402000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr6:26392800-26402000	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr6:26393000-26401600	Weak transcription	HUES48 Cell Line	embryonic stem cell
27	chr6:26393200-26401800	Weak transcription	Rectal Smooth Muscle	rectum
28	chr6:26393200-26402400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr6:26393400-26401800	Weak transcription	Fetal Muscle Leg	muscle
30	chr6:26393400-26402000	Weak transcription	HUES6 Cell Line	embryonic stem cell
31	chr6:26393600-26402400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr6:26393800-26401800	Weak transcription	Primary hematopoietic stem cells	blood
33	chr6:26393800-26401800	Weak transcription	Fetal Muscle Trunk	muscle
34	chr6:26393800-26402000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr6:26394000-26401600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr6:26394000-26401600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
37	chr6:26394000-26412000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr6:26394200-26401600	Weak transcription	Fetal Stomach	stomach
39	chr6:26394800-26402400	Weak transcription	Small Intestine	intestine
40	chr6:26395000-26401600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr6:26395000-26401600	Weak transcription	Adipose Nuclei	Adipose
42	chr6:26395000-26401800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr6:26395000-26402000	Weak transcription	Right Atrium	heart
44	chr6:26397200-26401800	Weak transcription	Duodenum Mucosa	Duodenum
45	chr6:26397400-26401600	Weak transcription	Fetal Intestine Large	intestine
46	chr6:26399000-26401800	Enhancers	K562	blood
47	chr6:26400000-26402200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr6:26400800-26401600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
49	chr6:26400800-26401600	Enhancers	Primary T helper cells PMA-I stimulated	--
50	chr6:26400800-26401600	Enhancers	Primary T killer naive cells fromperipheralblood	blood

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