Variant report

Variant	rs7356849
Chromosome Location	chr6:26396739-26396740
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:26395454..26397277-chr6:26501383..26504153,2	K562	blood:
2	chr6:26393793..26397119-chr6:26397996..26400964,7	K562	blood:
3	chr6:26394732..26396877-chr6:26400562..26403054,2	MCF-7	breast:
4	chr6:26395411..26398038-chr6:26426386..26428479,2	K562	blood:

Variant related genes	Relation type
ENSG00000026950	Chromatin interaction
ENSG00000124557	Chromatin interaction

Extended variants
information (count: 116 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:95)

rs_ID	r²[population]
rs10456047	0.93[CEU][hapmap]
rs10456331	0.93[CEU][hapmap]
rs10484441	0.93[CEU][hapmap]
rs10807008	0.93[CEU][hapmap];0.82[GIH][hapmap];0.83[TSI][hapmap];0.80[EUR][1000 genomes]
rs10946823	0.85[CEU][hapmap]
rs10946825	0.83[CEU][hapmap]
rs10946832	0.93[CEU][hapmap]
rs1131936	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12193283	0.93[CEU][hapmap]
rs12194036	0.93[CEU][hapmap]
rs12196371	0.93[CEU][hapmap]
rs12203176	0.85[CEU][hapmap]
rs12205476	0.88[EUR][1000 genomes]
rs12206621	0.83[CEU][hapmap]
rs12208211	0.93[CEU][hapmap]
rs12208788	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12211872	0.93[CEU][hapmap]
rs12214444	0.93[CEU][hapmap];0.83[TSI][hapmap]
rs12661560	0.93[CEU][hapmap]
rs12662604	0.91[EUR][1000 genomes]
rs12664899	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs13437351	1.00[JPT][hapmap]
rs16891666	1.00[JPT][hapmap]
rs17537465	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs17610161	0.93[CEU][hapmap];0.82[GIH][hapmap]
rs1884945	0.93[CEU][hapmap]
rs2281027	1.00[JPT][hapmap]
rs2393664	0.87[CEU][hapmap]
rs2893849	0.86[CEU][hapmap];0.83[CHD][hapmap]
rs2893856	0.86[CEU][hapmap];0.83[CHD][hapmap]
rs2893857	0.93[CEU][hapmap]
rs3734541	1.00[JPT][hapmap]
rs3757141	1.00[JPT][hapmap]
rs3757147	1.00[JPT][hapmap]
rs3846841	1.00[JPT][hapmap]
rs3846842	1.00[JPT][hapmap]
rs3857549	1.00[JPT][hapmap]
rs3902051	1.00[CEU][hapmap];0.82[GIH][hapmap];0.87[TSI][hapmap];0.88[EUR][1000 genomes]
rs41266835	0.88[EUR][1000 genomes]
rs4476815	1.00[JPT][hapmap]
rs4711108	0.92[CEU][hapmap];0.80[EUR][1000 genomes]
rs4711110	0.92[CEU][hapmap]
rs4712986	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.95[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4712988	1.00[CEU][hapmap];0.85[GIH][hapmap];0.86[TSI][hapmap];0.81[AFR][1000 genomes]
rs4712989	0.91[EUR][1000 genomes]
rs4712990	0.93[CEU][hapmap];0.83[TSI][hapmap]
rs4712999	0.85[CEU][hapmap]
rs4713000	0.92[CEU][hapmap]
rs4713001	0.93[CEU][hapmap]
rs56023587	0.91[EUR][1000 genomes]
rs6456716	0.85[CEU][hapmap]
rs6456720	1.00[JPT][hapmap]
rs6456723	0.86[CEU][hapmap]
rs6456724	0.86[CEU][hapmap]
rs6456725	1.00[JPT][hapmap]
rs6456726	1.00[JPT][hapmap]
rs6901118	1.00[JPT][hapmap]
rs6907857	1.00[JPT][hapmap]
rs6910921	1.00[JPT][hapmap]
rs6910993	1.00[JPT][hapmap]
rs6911470	1.00[JPT][hapmap]
rs6912934	0.86[CEU][hapmap];0.83[CHD][hapmap]
rs6922353	0.83[ASN][1000 genomes]
rs6929846	0.93[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs72841540	0.84[EUR][1000 genomes]
rs7355	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7356982	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7751645	1.00[JPT][hapmap]
rs7768108	0.93[CEU][hapmap];0.83[TSI][hapmap]
rs7769926	1.00[JPT][hapmap]
rs7773913	1.00[JPT][hapmap]
rs882010	0.93[CEU][hapmap]
rs9104	0.85[CEU][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap]
rs9295690	0.87[CEU][hapmap]
rs9295692	1.00[JPT][hapmap]
rs9461245	0.85[CEU][hapmap]
rs9461252	1.00[JPT][hapmap]
rs9461253	1.00[JPT][hapmap]
rs9461254	1.00[JPT][hapmap]
rs9467716	0.85[CEU][hapmap]
rs9467717	0.83[CEU][hapmap]
rs9467721	0.85[CEU][hapmap]
rs9467748	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs9467750	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9467751	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9467753	1.00[JPT][hapmap]
rs9467757	1.00[JPT][hapmap]
rs9467759	0.86[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs9467760	0.85[JPT][hapmap]
rs9467761	1.00[JPT][hapmap]
rs9467768	1.00[JPT][hapmap]
rs9467771	1.00[JPT][hapmap]
rs9467788	1.00[JPT][hapmap]
rs9467803	1.00[JPT][hapmap]
rs9688949	0.85[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:21 , 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
21	nsv970087	chr6:26392332-26397363	Weak transcription Enhancers Strong transcription Genic enhancers	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7356849	BTN3A1	Cis_1M	lymphoblastoid	RTeQTL
rs7356849	HIST1H4E	cis	cerebellum	SCAN
rs7356849	BTN2A2	Cis_1M	lymphoblastoid	RTeQTL
rs7356849	BTN2A1	cis	parietal	SCAN

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:26384200-26400800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
2	chr6:26384200-26400800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr6:26384200-26401000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr6:26384200-26401400	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr6:26384200-26402000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr6:26384200-26402400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr6:26384200-26402400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr6:26384200-26402400	Weak transcription	Pancreas	Pancrea
9	chr6:26384400-26401400	Weak transcription	Brain Angular Gyrus	brain
10	chr6:26384400-26402000	Weak transcription	Fetal Kidney	kidney
11	chr6:26384600-26400800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr6:26384600-26401800	Weak transcription	Fetal Lung	lung
13	chr6:26385200-26401000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr6:26385200-26401400	Weak transcription	Brain Substantia Nigra	brain
15	chr6:26385200-26401800	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr6:26385400-26400800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
17	chr6:26385800-26402000	Weak transcription	Colonic Mucosa	Colon
18	chr6:26388200-26402000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr6:26388800-26401800	Weak transcription	Placenta	Placenta
20	chr6:26389000-26396800	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr6:26391200-26401600	Weak transcription	Aorta	Aorta
22	chr6:26391200-26401600	Weak transcription	Liver	Liver
23	chr6:26391200-26401800	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr6:26391200-26402000	Weak transcription	Right Ventricle	heart
25	chr6:26391200-26402400	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr6:26391800-26402000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr6:26392200-26402000	Weak transcription	HUES64 Cell Line	embryonic stem cell
28	chr6:26392200-26402000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
29	chr6:26392200-26402000	Weak transcription	Left Ventricle	heart
30	chr6:26392400-26401600	Weak transcription	Brain Anterior Caudate	brain
31	chr6:26392400-26401600	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr6:26392400-26401800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr6:26392600-26400800	Weak transcription	Primary T cells fromperipheralblood	blood
34	chr6:26392600-26400800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
35	chr6:26392600-26400800	Weak transcription	Primary T helper cells PMA-I stimulated	--
36	chr6:26392600-26401000	Weak transcription	Primary T helper cells fromperipheralblood	blood
37	chr6:26392600-26401600	Weak transcription	Colon Smooth Muscle	Colon
38	chr6:26392800-26402000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
39	chr6:26392800-26402000	Weak transcription	Duodenum Smooth Muscle	Duodenum
40	chr6:26393000-26401600	Weak transcription	HUES48 Cell Line	embryonic stem cell
41	chr6:26393200-26401800	Weak transcription	Rectal Smooth Muscle	rectum
42	chr6:26393200-26402400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr6:26393400-26398600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr6:26393400-26401000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr6:26393400-26401000	Weak transcription	Thymus	Thymus
46	chr6:26393400-26401400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr6:26393400-26401800	Weak transcription	Fetal Muscle Leg	muscle
48	chr6:26393400-26402000	Weak transcription	HUES6 Cell Line	embryonic stem cell
49	chr6:26393600-26397200	Enhancers	Duodenum Mucosa	Duodenum
50	chr6:26393600-26401400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood

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