Variant report

Variant	rs2076029
Chromosome Location	chr6:26390830-26390831
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:26385648..26389626-chr6:26390686..26394827,7	K562	blood:
2	chr6:26390334..26392111-chr6:26392874..26394423,2	K562	blood:
3	chr6:26390074..26392884-chr6:26401508..26403224,2	K562	blood:
4	chr6:26378930..26384775-chr6:26385231..26390850,8	MCF-7	breast:
5	chr6:26390542..26392521-chr6:26396863..26399641,3	K562	blood:
6	chr6:26384661..26390027-chr6:26390440..26394308,9	K562	blood:

Variant related genes	Relation type
ENSG00000026950	Chromatin interaction
ENSG00000124508	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10946813	0.92[CEU][hapmap]
rs10946817	0.85[CEU][hapmap]
rs12199613	0.85[CEU][hapmap]
rs12214031	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs12663780	0.81[AFR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1614887	0.80[JPT][hapmap]
rs2072804	0.89[ASN][1000 genomes]
rs2237236	0.96[CEU][hapmap];0.82[CHD][hapmap];0.83[JPT][hapmap];0.83[MKK][hapmap];0.91[TSI][hapmap];0.85[YRI][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3208733	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3734536	0.85[CEU][hapmap]
rs3799379	0.88[CEU][hapmap];0.88[CHB][hapmap];0.94[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3846845	0.96[CEU][hapmap];0.88[CHB][hapmap];0.94[JPT][hapmap];0.89[YRI][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3846846	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4320356	0.83[ASW][hapmap];0.96[CEU][hapmap];0.88[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.85[MKK][hapmap];0.93[TSI][hapmap];0.85[YRI][hapmap];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4712984	0.92[ASW][hapmap];1.00[CEU][hapmap];0.83[CHB][hapmap];0.91[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap]
rs4712987	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4712998	0.81[CHB][hapmap]
rs66972160	0.80[EUR][1000 genomes]
rs6907924	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7356988	1.00[CEU][hapmap];0.88[CHB][hapmap];0.89[JPT][hapmap];0.84[YRI][hapmap];0.85[AFR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9366657	0.83[ASW][hapmap];0.96[CEU][hapmap];0.88[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.85[MKK][hapmap];0.91[TSI][hapmap];0.85[YRI][hapmap];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9379860	0.92[CEU][hapmap];0.80[EUR][1000 genomes]
rs9379874	0.96[CEU][hapmap];0.88[CHB][hapmap];0.94[JPT][hapmap];0.85[YRI][hapmap];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9393709	0.85[CEU][hapmap]
rs9467722	0.92[CEU][hapmap];0.80[EUR][1000 genomes]
rs9467732	0.85[ASN][1000 genomes]
rs9467736	0.88[ASN][1000 genomes]
rs9467737	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9688946	0.84[CEU][hapmap]

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:11)

SNP	Gene	Cis/trans	Tissue	Source
rs2076029	BTN3A1	cis	parietal	SCAN
rs2076029	CHRNA1	trans	cerebellum	SCAN
rs2076029	HMGN4	cis	parietal	SCAN
rs2076029	BTN3A1	cis	cerebellum	SCAN
rs2076029	ZKSCAN3	cis	cerebellum	SCAN
rs2076029	BTN3A3	cis	cerebellum	SCAN
rs2076029	BTN3A3	cis	parietal	SCAN
rs2076029	BTN3A2	cis	lymphoblastoid	seeQTL
rs2076029	ZSCAN23	cis	cerebellum	SCAN
rs2076029	BTN2A2	Cis_1M	lymphoblastoid	RTeQTL
rs2076029	BTN2A2	cis	cerebellum	SCAN

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:26384200-26392200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr6:26384200-26393000	Weak transcription	Fetal Brain Female	brain
3	chr6:26384200-26393200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr6:26384200-26394600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr6:26384200-26394600	Weak transcription	Right Atrium	heart
6	chr6:26384200-26400800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr6:26384200-26400800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr6:26384200-26401000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr6:26384200-26401400	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr6:26384200-26402000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr6:26384200-26402400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr6:26384200-26402400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr6:26384200-26402400	Weak transcription	Pancreas	Pancrea
14	chr6:26384400-26394200	Weak transcription	HUVEC	blood vessel
15	chr6:26384400-26401400	Weak transcription	Brain Angular Gyrus	brain
16	chr6:26384400-26402000	Weak transcription	Fetal Kidney	kidney
17	chr6:26384600-26394400	Weak transcription	Fetal Intestine Large	intestine
18	chr6:26384600-26394400	Weak transcription	NHDF-Ad	bronchial
19	chr6:26384600-26394600	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr6:26384600-26400800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
21	chr6:26384600-26401800	Weak transcription	Fetal Lung	lung
22	chr6:26385200-26394600	Weak transcription	Brain Germinal Matrix	brain
23	chr6:26385200-26401000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
24	chr6:26385200-26401400	Weak transcription	Brain Substantia Nigra	brain
25	chr6:26385200-26401800	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr6:26385400-26400800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
27	chr6:26385800-26402000	Weak transcription	Colonic Mucosa	Colon
28	chr6:26386800-26392200	Strong transcription	Primary B cells from cord blood	blood
29	chr6:26387000-26394600	Weak transcription	Small Intestine	intestine
30	chr6:26387800-26393400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr6:26388000-26392800	Strong transcription	Fetal Muscle Leg	muscle
32	chr6:26388000-26393800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr6:26388000-26394200	Strong transcription	Fetal Stomach	stomach
34	chr6:26388200-26392600	Strong transcription	Primary T cells fromperipheralblood	blood
35	chr6:26388200-26393400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr6:26388200-26393400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr6:26388200-26393400	Strong transcription	Fetal Intestine Small	intestine
38	chr6:26388200-26393800	Strong transcription	Primary T cells from cord blood	blood
39	chr6:26388200-26393800	Strong transcription	Fetal Muscle Trunk	muscle
40	chr6:26388200-26393800	Strong transcription	Dnd41	blood
41	chr6:26388200-26402000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
42	chr6:26388400-26393200	Strong transcription	Primary B cells from peripheral blood	blood
43	chr6:26388400-26395000	Weak transcription	H1 Cell Line	embryonic stem cell
44	chr6:26388600-26393000	Strong transcription	HUES48 Cell Line	embryonic stem cell
45	chr6:26388600-26393800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr6:26388800-26391600	Weak transcription	Primary hematopoietic stem cells	blood
47	chr6:26388800-26392400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr6:26388800-26393400	Weak transcription	HSMM	muscle
49	chr6:26388800-26394200	Weak transcription	A549	lung
50	chr6:26388800-26401800	Weak transcription	Placenta	Placenta

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