Variant report

Variant	rs12199613
Chromosome Location	chr6:26367218-26367219
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	MXI1	chr6:26364117-26367241	SK-N-SH	brain:	n/a	chr6:26365782-26365791
2	RFX5	chr6:26362983-26367827	IMR90	lung:	n/a	chr6:26365394-26365403 chr6:26365363-26365372 chr6:26365370-26365378 chr6:26365360-26365375
3	CTCF	chr6:26367140-26367290	GM12864	blood:	n/a	n/a
4	RFX5	chr6:26362934-26367943	SK-N-SH	brain:	n/a	chr6:26365394-26365403 chr6:26365363-26365372 chr6:26365370-26365378 chr6:26365360-26365375

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:26365788..26367808-chr6:26370738..26372498,2	K562	blood:

Variant related genes	Relation type
ENSG00000215979	TF binding region
BTN3A2	TF binding region
ENSG00000186470	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10456045	0.86[JPT][hapmap]
rs10946812	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10946813	0.81[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.85[YRI][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10946817	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12214031	1.00[ASW][hapmap];0.92[CEU][hapmap];0.87[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.91[MEX][hapmap];0.96[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13218591	0.81[MKK][hapmap];0.83[TSI][hapmap]
rs1985732	0.93[GIH][hapmap]
rs2076029	0.85[CEU][hapmap]
rs2237236	0.81[CEU][hapmap]
rs34565965	0.81[ASN][1000 genomes]
rs3734536	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3846845	0.81[CEU][hapmap]
rs4320356	0.81[CEU][hapmap]
rs4712980	0.90[GIH][hapmap];0.89[LWK][hapmap];0.81[AFR][1000 genomes]
rs4712981	0.91[GIH][hapmap]
rs4712984	0.85[CEU][hapmap]
rs4712987	0.85[CEU][hapmap];0.81[JPT][hapmap]
rs66972160	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6933583	0.91[GIH][hapmap];0.87[LWK][hapmap];0.81[AFR][1000 genomes]
rs6935803	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6936006	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7356988	0.88[CEU][hapmap]
rs9348710	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9366657	0.81[CEU][hapmap]
rs9379860	0.92[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9379870	0.91[GIH][hapmap];0.87[LWK][hapmap]
rs9379874	0.80[CEU][hapmap]
rs9393709	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9467722	0.92[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9688946	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs12199613	HMGN4	cis	parietal	SCAN
rs12199613	BTN2A2	Cis_1M	lymphoblastoid	RTeQTL
rs12199613	BTN2A2	cis	cerebellum	SCAN
rs12199613	BTN3A1	cis	parietal	SCAN
rs12199613	BTN3A3	cis	parietal	SCAN
rs12199613	BTN3A2	Cis_1M	lymphoblastoid	RTeQTL
rs12199613	ZNF193	cis	parietal	SCAN
rs12199613	BTN3A3	cis	cerebellum	SCAN
rs12199613	BTN3A2	cis	lymphoblastoid	seeQTL

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:26364800-26367600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr6:26365000-26367800	Active TSS	Rectal Mucosa Donor 29	rectum
3	chr6:26365600-26367600	Flanking Active TSS	Primary B cells from cord blood	blood
4	chr6:26365600-26367800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr6:26365800-26367600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
6	chr6:26365800-26367600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr6:26365800-26375200	Weak transcription	Aorta	Aorta
8	chr6:26366000-26367800	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr6:26366000-26368800	Weak transcription	Fetal Stomach	stomach
10	chr6:26366000-26369400	Weak transcription	Brain Cingulate Gyrus	brain
11	chr6:26366000-26369400	Weak transcription	Fetal Lung	lung
12	chr6:26366000-26369400	Weak transcription	Fetal Muscle Trunk	muscle
13	chr6:26366000-26369400	Weak transcription	Lung	lung
14	chr6:26366000-26369400	Weak transcription	Ovary	ovary
15	chr6:26366000-26369800	Weak transcription	Brain Angular Gyrus	brain
16	chr6:26366000-26369800	Weak transcription	Brain Substantia Nigra	brain
17	chr6:26366000-26373200	Weak transcription	Colonic Mucosa	Colon
18	chr6:26366000-26373800	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr6:26366000-26374800	Weak transcription	Esophagus	oesophagus
20	chr6:26366000-26375000	Weak transcription	Brain Anterior Caudate	brain
21	chr6:26366000-26375600	Weak transcription	Gastric	stomach
22	chr6:26366000-26382600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr6:26366000-26383000	Weak transcription	Brain Hippocampus Middle	brain
24	chr6:26366000-26383200	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr6:26366000-26383200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr6:26366000-26383200	Weak transcription	Pancreas	Pancrea
27	chr6:26366000-26383200	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr6:26366000-26383200	Weak transcription	HSMMtube	muscle
29	chr6:26366000-26383400	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr6:26366200-26367400	Flanking Active TSS	Primary T cells from cord blood	blood
31	chr6:26366200-26367600	Flanking Active TSS	Dnd41	blood
32	chr6:26366200-26367800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
33	chr6:26366200-26367800	Enhancers	HepG2	liver
34	chr6:26366200-26367800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
35	chr6:26366200-26369400	Weak transcription	Placenta	Placenta
36	chr6:26366200-26371200	Weak transcription	A549	lung
37	chr6:26366200-26374600	Weak transcription	Muscle Satellite Cultured Cells	--
38	chr6:26366200-26374800	Weak transcription	Stomach Smooth Muscle	stomach
39	chr6:26366200-26375000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr6:26366200-26375200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr6:26366200-26375800	Weak transcription	NH-A	brain
42	chr6:26366200-26382400	Weak transcription	Cortex derived primary cultured neurospheres	brain
43	chr6:26366200-26383200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr6:26366200-26383200	Weak transcription	Pancreatic Islets	Pancreatic Islet
45	chr6:26366400-26367800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
46	chr6:26366400-26367800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
47	chr6:26366400-26368000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
48	chr6:26366400-26372600	Weak transcription	Duodenum Smooth Muscle	Duodenum
49	chr6:26366600-26367400	Flanking Active TSS	Primary hematopoietic stem cells	blood
50	chr6:26366600-26367800	Enhancers	K562	blood

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