Variant report

Variant	rs6929846
Chromosome Location	chr6:26458265-26458266
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:62609075..62609632-chr6:26457866..26458649,2	NB4	blood:
2	chr6:26449553..26453974-chr6:26454911..26459271,5	K562	blood:
3	chr6:26457960..26461047-chr6:26519488..26522400,3	MCF-7	breast:
4	chr6:26158231..26160273-chr6:26456660..26458707,2	K562	blood:

Variant related genes	Relation type
ENSG00000158373	Chromatin interaction
ENSG00000133316	Chromatin interaction
ENSG00000111801	Chromatin interaction
ENSG00000199289	Chromatin interaction
ENSG00000228223	Chromatin interaction

Extended variants
information (count: 162 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:141)

rs_ID	r²[population]
rs10447390	0.86[CEU][hapmap]
rs10447391	0.86[CEU][hapmap]
rs10456047	0.86[CEU][hapmap]
rs10456331	0.86[CEU][hapmap]
rs10484441	0.86[CEU][hapmap]
rs10807008	0.86[CEU][hapmap]
rs10946820	0.86[CEU][hapmap]
rs10946821	0.86[CEU][hapmap]
rs10946823	0.93[CEU][hapmap]
rs10946824	0.86[CEU][hapmap]
rs10946825	0.83[CEU][hapmap]
rs10946826	0.86[CEU][hapmap]
rs10946827	0.86[CEU][hapmap]
rs10946829	0.86[CEU][hapmap]
rs10946832	0.86[CEU][hapmap]
rs1131936	0.93[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs12191917	0.86[CEU][hapmap]
rs12193283	0.86[CEU][hapmap]
rs12194001	0.83[CEU][hapmap]
rs12194036	0.86[CEU][hapmap]
rs12194073	0.86[CEU][hapmap]
rs12196371	0.86[CEU][hapmap]
rs12198993	0.86[CEU][hapmap]
rs12201546	0.86[CEU][hapmap]
rs12206812	0.86[CEU][hapmap]
rs12207930	0.86[CEU][hapmap]
rs12208211	0.86[CEU][hapmap]
rs12208788	0.93[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs12211872	0.86[CEU][hapmap]
rs12214444	0.86[CEU][hapmap]
rs12214486	0.86[CEU][hapmap]
rs12214924	0.86[CEU][hapmap]
rs12661560	0.86[CEU][hapmap]
rs12664899	0.93[CEU][hapmap]
rs13437351	1.00[JPT][hapmap]
rs13978	1.00[JPT][hapmap]
rs16891666	1.00[JPT][hapmap]
rs17537465	0.93[CEU][hapmap]
rs17539219	0.86[CEU][hapmap]
rs17610161	0.86[CEU][hapmap]
rs17611220	0.86[CEU][hapmap]
rs17611438	0.86[CEU][hapmap]
rs1884945	0.86[CEU][hapmap]
rs2281027	1.00[JPT][hapmap]
rs2393652	0.86[CEU][hapmap]
rs2393664	0.93[CEU][hapmap]
rs2893844	0.85[CEU][hapmap]
rs2893845	0.86[CEU][hapmap]
rs2893847	0.86[CEU][hapmap]
rs2893848	0.86[CEU][hapmap]
rs2893849	0.93[CEU][hapmap];0.83[CHD][hapmap];0.94[GIH][hapmap];0.82[EUR][1000 genomes]
rs2893856	0.93[CEU][hapmap];0.83[CHD][hapmap];0.90[GIH][hapmap];0.83[EUR][1000 genomes]
rs2893857	0.86[CEU][hapmap]
rs3198487	0.85[CEU][hapmap]
rs3208734	0.86[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]
rs3846843	0.86[CEU][hapmap]
rs3846844	0.86[CEU][hapmap]
rs3846847	0.86[CEU][hapmap]
rs3846848	0.86[CEU][hapmap]
rs3846849	0.86[CEU][hapmap]
rs3857549	1.00[JPT][hapmap]
rs3902051	0.93[CEU][hapmap]
rs4083469	0.86[CEU][hapmap]
rs4476815	1.00[JPT][hapmap]
rs4609015	0.86[CEU][hapmap]
rs4711108	0.85[CEU][hapmap]
rs4711109	0.86[CEU][hapmap]
rs4711110	0.85[CEU][hapmap]
rs4711111	0.86[CEU][hapmap]
rs4712986	0.93[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs4712988	0.93[CEU][hapmap]
rs4712990	0.86[CEU][hapmap]
rs4712993	0.86[CEU][hapmap]
rs4712994	0.86[CEU][hapmap]
rs4712996	0.86[CEU][hapmap]
rs4712999	0.93[CEU][hapmap]
rs4713000	0.85[CEU][hapmap]
rs4713001	0.86[CEU][hapmap]
rs6456720	1.00[JPT][hapmap]
rs6456722	0.85[CEU][hapmap]
rs6456723	0.93[CEU][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6456724	0.93[CEU][hapmap];0.94[GIH][hapmap];0.83[EUR][1000 genomes]
rs6456725	1.00[JPT][hapmap]
rs6456726	1.00[JPT][hapmap]
rs6900725	0.86[CEU][hapmap]
rs6901118	1.00[JPT][hapmap]
rs6901245	0.84[CEU][hapmap]
rs6902081	1.00[JPT][hapmap]
rs6907857	1.00[JPT][hapmap]
rs6910023	0.86[CEU][hapmap]
rs6910849	1.00[JPT][hapmap]
rs6910871	1.00[JPT][hapmap]
rs6910921	1.00[JPT][hapmap]
rs6910993	1.00[JPT][hapmap]
rs6911470	1.00[JPT][hapmap]
rs6911476	1.00[JPT][hapmap]
rs6912934	0.93[CEU][hapmap];0.83[CHD][hapmap];0.90[GIH][hapmap];0.80[EUR][1000 genomes]
rs6920948	0.83[EUR][1000 genomes]
rs6920982	0.83[EUR][1000 genomes]
rs6920986	0.86[CEU][hapmap]
rs6922353	0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6926878	0.86[CEU][hapmap]
rs6928454	0.86[CEU][hapmap]
rs7355	0.93[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs7356849	0.93[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs7356982	0.87[CEU][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs7744254	0.86[CEU][hapmap]
rs7745238	0.86[CEU][hapmap]
rs7745767	0.86[CEU][hapmap]
rs7751280	0.86[CEU][hapmap]
rs7751645	1.00[JPT][hapmap]
rs7768108	0.86[CEU][hapmap]
rs7769926	1.00[JPT][hapmap]
rs7770214	0.86[CEU][hapmap]
rs7773913	1.00[JPT][hapmap]
rs882010	0.86[CEU][hapmap]
rs9104	1.00[JPT][hapmap]
rs9295690	0.93[CEU][hapmap]
rs9295692	1.00[JPT][hapmap]
rs9295700	1.00[JPT][hapmap]
rs9393722	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9461252	1.00[JPT][hapmap]
rs9461253	1.00[JPT][hapmap]
rs9461254	1.00[JPT][hapmap]
rs9467748	0.80[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs9467750	0.81[ASN][1000 genomes]
rs9467751	0.81[ASN][1000 genomes]
rs9467753	1.00[JPT][hapmap]
rs9467757	1.00[JPT][hapmap]
rs9467759	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.97[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]

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	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
7	esv2763996	chr6:26423901-26465384	Enhancers Genic enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
8	nsv1017824	chr6:26425410-26465384	Strong transcription Active TSS Weak transcription Flanking Active TSS Enhancers 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	16 gene(s)	inside rSNPs	diseases
9	nsv1030289	chr6:26428314-26464017	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
10	nsv1033003	chr6:26428314-26465384	Transcr. at gene 5' and 3' Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
11	nsv1031229	chr6:26428314-26467182	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
12	nsv1031238	chr6:26428314-26471596	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
13	nsv1024483	chr6:26429262-26465384	Flanking Active TSS Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Weak transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
14	nsv1034561	chr6:26429262-26467182	Enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
15	nsv528172	chr6:26430981-26463660	Genic enhancers Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats 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	15 gene(s)	inside rSNPs	diseases
16	nsv1029357	chr6:26432815-26464789	Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
17	nsv1023581	chr6:26432815-26465384	Enhancers Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
18	nsv1024222	chr6:26432815-26467182	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
19	nsv1022309	chr6:26434914-26464789	Enhancers Strong transcription Active TSS Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
20	nsv601185	chr6:26455811-26465384	Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Weak transcription Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
21	nsv965689	chr6:26457033-26469487	Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs6929846	BTN3A2	cis	multi-tissue	Pritchard
rs6929846	BTN2A1	cis	parietal	SCAN
rs6929846	BTN2A2	cis	multi-tissue	Pritchard
rs6929846	BTN3A2	cis	parietal	SCAN
rs6929846	BTN3A3	cis	cerebellum	SCAN
rs6929846	BTN2A1	cis	multi-tissue	Pritchard
rs6929846	BTN2A1	cis	Whole Blood	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:26457600-26459000	Active TSS	H9 Cell Line	embryonic stem cell
2	chr6:26457600-26459200	Active TSS	ES-I3 Cell Line	embryonic stem cell
3	chr6:26457600-26459200	Active TSS	Primary T cells from cord blood	blood
4	chr6:26457600-26459200	Active TSS	A549	lung
5	chr6:26457600-26459400	Active TSS	iPS-15b Cell Line	embryonic stem cell
6	chr6:26457600-26459400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr6:26457600-26459400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
8	chr6:26457600-26459400	Active TSS	Fetal Brain Female	brain
9	chr6:26457600-26459400	Active TSS	Fetal Kidney	kidney
10	chr6:26457600-26460400	Active TSS	Pancreatic Islets	Pancreatic Islet
11	chr6:26457800-26458600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
12	chr6:26457800-26458600	Bivalent/Poised TSS	HepG2	liver
13	chr6:26457800-26458800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr6:26457800-26458800	Active TSS	Liver	Liver
15	chr6:26457800-26458800	Active TSS	Small Intestine	intestine
16	chr6:26457800-26459000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr6:26457800-26459000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr6:26457800-26459000	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
19	chr6:26457800-26459000	Active TSS	Brain Anterior Caudate	brain
20	chr6:26457800-26459000	Active TSS	Duodenum Mucosa	Duodenum
21	chr6:26457800-26459000	Active TSS	Pancreas	Pancrea
22	chr6:26457800-26459000	Active TSS	Spleen	Spleen
23	chr6:26457800-26459200	Active TSS	H1 Cell Line	embryonic stem cell
24	chr6:26457800-26459200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
25	chr6:26457800-26459200	Active TSS	Brain Substantia Nigra	brain
26	chr6:26457800-26459200	Active TSS	Fetal Intestine Small	intestine
27	chr6:26457800-26459200	Active TSS	Fetal Stomach	stomach
28	chr6:26457800-26459200	Active TSS	Ovary	ovary
29	chr6:26457800-26459200	Active TSS	Placenta Amnion	Placenta Amnion
30	chr6:26457800-26459200	Active TSS	Rectal Mucosa Donor 29	rectum
31	chr6:26457800-26459200	Active TSS	Thymus	Thymus
32	chr6:26457800-26459400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr6:26457800-26459400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr6:26457800-26459400	Active TSS	Brain Angular Gyrus	brain
35	chr6:26457800-26459400	Active TSS	Brain Hippocampus Middle	brain
36	chr6:26457800-26459400	Active TSS	Brain Inferior Temporal Lobe	brain
37	chr6:26457800-26459400	Active TSS	Colonic Mucosa	Colon
38	chr6:26457800-26459400	Active TSS	Esophagus	oesophagus
39	chr6:26457800-26459400	Active TSS	Fetal Intestine Large	intestine
40	chr6:26457800-26459400	Active TSS	Left Ventricle	heart
41	chr6:26457800-26459400	Active TSS	Psoas Muscle	Psoas
42	chr6:26457800-26459400	Active TSS	Right Atrium	heart
43	chr6:26457800-26459400	Active TSS	Right Ventricle	heart
44	chr6:26457800-26459400	Active TSS	Skeletal Muscle Female	skeletal muscle
45	chr6:26457800-26459600	Active TSS	HUES48 Cell Line	embryonic stem cell
46	chr6:26457800-26459600	Active TSS	iPS-20b Cell Line	embryonic stem cell
47	chr6:26457800-26459600	Active TSS	Aorta	Aorta
48	chr6:26458000-26458400	Active TSS	Primary B cells from cord blood	blood
49	chr6:26458000-26458600	Active TSS	Primary hematopoietic stem cells	blood
50	chr6:26458000-26458600	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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