Variant report

Variant	rs564405
Chromosome Location	chr6:149641200-149641201
allele	A/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	NFATC1	chr6:149639550-149641270	GM12878	blood:	n/a	n/a
2	NFIC	chr6:149639135-149641240	GM12878	blood:	n/a	n/a
3	NFATC1	chr6:149640291-149641234	GM12878	blood:	n/a	n/a
4	IKZF1	chr6:149641055-149641348	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:149351823..149355344-chr6:149638842..149641991,4	MCF-7	breast:

Variant related genes	Relation type
TAB2	TF binding region
ENSG00000236591	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs17086451	0.81[ASN][1000 genomes]
rs2341783	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2341784	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2744427	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2744428	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2744433	0.81[ASN][1000 genomes]
rs2744434	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2789487	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2789489	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2789490	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2789500	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3734296	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4360154	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs472620	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs472810	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs474369	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs478531	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs478767	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs480526	0.97[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs480778	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs481769	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4897117	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs490529	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs492956	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs494340	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs501926	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs504762	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs511105	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs513923	0.81[ASN][1000 genomes]
rs515133	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs518879	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs522646	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs527971	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs532008	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs532250	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs533026	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs538386	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs554926	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs556335	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs559052	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs559204	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs565825	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs570442	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs588028	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs60006373	0.81[ASN][1000 genomes]
rs600739	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs630642	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs641068	0.81[ASN][1000 genomes]
rs652514	0.81[ASN][1000 genomes]
rs652921	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs663625	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs681919	0.83[EUR][1000 genomes]
rs92605	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9373591	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs9377216	0.81[ASN][1000 genomes]
rs9390676	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9399686	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9404032	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9404034	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9404035	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1024776	chr6:149398652-149654593	Weak transcription Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv1015360	chr6:149609804-149649982	Weak transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv1024106	chr6:149622349-149745053	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS 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	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs564405	MAP3K7IP2,TAB2	cis	brain	BrainEAC

Chromatin state (count:159 , 50 per page) page: 1 2 3 4

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:149637400-149641200	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr6:149637400-149641200	Active TSS	Brain Angular Gyrus	brain
3	chr6:149637400-149641200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
4	chr6:149637400-149641200	Active TSS	Duodenum Smooth Muscle	Duodenum
5	chr6:149637400-149641200	Active TSS	Stomach Smooth Muscle	stomach
6	chr6:149637400-149641200	Active TSS	HSMMtube	muscle
7	chr6:149637400-149641200	Active TSS	NH-A	brain
8	chr6:149637400-149641600	Active TSS	Brain Substantia Nigra	brain
9	chr6:149637400-149642000	Active TSS	Breast Myoepithelial Primary Cells	Breast
10	chr6:149637400-149642600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr6:149637600-149641200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr6:149637600-149641200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr6:149637600-149641200	Active TSS	Aorta	Aorta
14	chr6:149637600-149641200	Active TSS	Fetal Kidney	kidney
15	chr6:149637600-149641200	Active TSS	NHLF	lung
16	chr6:149637600-149641400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr6:149637600-149641400	Active TSS	Brain Inferior Temporal Lobe	brain
18	chr6:149637600-149642000	Active TSS	GM12878-XiMat	blood
19	chr6:149637800-149641200	Active TSS	Pancreatic Islets	Pancreatic Islet
20	chr6:149637800-149641200	Active TSS	HMEC	breast
21	chr6:149637800-149641400	Active TSS	Primary T helper cells PMA-I stimulated	--
22	chr6:149638000-149641200	Active TSS	Primary T cells fromperipheralblood	blood
23	chr6:149639600-149641200	Flanking Active TSS	Primary B cells from cord blood	blood
24	chr6:149639800-149641200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
25	chr6:149639800-149641200	Flanking Active TSS	HUVEC	blood vessel
26	chr6:149639800-149641800	Flanking Active TSS	Dnd41	blood
27	chr6:149639800-149642000	Flanking Active TSS	Primary T cells from cord blood	blood
28	chr6:149639800-149643400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr6:149640000-149641200	Active TSS	Psoas Muscle	Psoas
30	chr6:149640000-149641200	Weak transcription	Spleen	Spleen
31	chr6:149640000-149641600	Flanking Active TSS	Primary hematopoietic stem cells	blood
32	chr6:149640000-149642200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
33	chr6:149640000-149649400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr6:149640200-149641200	Weak transcription	Lung	lung
35	chr6:149640200-149641200	Weak transcription	Pancreas	Pancrea
36	chr6:149640200-149641200	Weak transcription	Sigmoid Colon	Sigmoid Colon
37	chr6:149640200-149641200	Weak transcription	Small Intestine	intestine
38	chr6:149640200-149641800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
39	chr6:149640200-149645600	Weak transcription	Left Ventricle	heart
40	chr6:149640200-149655400	Weak transcription	Esophagus	oesophagus
41	chr6:149640200-149655600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr6:149640400-149641200	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
43	chr6:149640400-149641200	Flanking Active TSS	Osteobl	bone
44	chr6:149640400-149641400	Active TSS	Primary T regulatory cells fromperipheralblood	blood
45	chr6:149640400-149641400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr6:149640400-149642000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
47	chr6:149640400-149642200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr6:149640400-149642800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
49	chr6:149640400-149645600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
50	chr6:149640400-149648600	Weak transcription	Right Ventricle	heart

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