Variant report

Variant	rs9380270
Chromosome Location	chr6:11412982-11412983
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	RCOR1	chr6:11412878-11413302	K562	blood:	n/a	n/a
2	TCF12	chr6:11412003-11412995	ECC-1	luminal epithelium:	n/a	n/a
3	EP300	chr6:11412935-11413163	K562	blood:	n/a	n/a
4	ATF1	chr6:11412921-11413267	K562	blood:	n/a	n/a
5	GATA3	chr6:11411945-11413031	SK-N-SH	brain:	n/a	chr6:11412685-11412692 chr6:11412818-11412831
6	RCOR1	chr6:11412949-11413243	K562	blood:	n/a	n/a
7	EP300	chr6:11411946-11413018	ECC-1	luminal epithelium:	n/a	chr6:11412550-11412560 chr6:11412895-11412905
8	CCNT2	chr6:11412911-11413220	K562	blood:	n/a	n/a
9	FOXM1	chr6:11411996-11413024	ECC-1	luminal epithelium:	n/a	n/a
10	BHLHE40	chr6:11412943-11413186	K562	blood:	n/a	n/a
11	TBL1XR1	chr6:11412903-11413224	K562	blood:	n/a	n/a
12	NFIC	chr6:11412034-11412988	ECC-1	luminal epithelium:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:11229922..11234167-chr6:11411662..11415515,7	MCF-7	breast:
2	chr6:11387321..11394874-chr6:11409302..11416244,8	MCF-7	breast:
3	chr6:11216036..11217997-chr6:11412401..11415164,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000233656	TF binding region
ENSG00000111859	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs4330532	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4368806	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4370358	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4713491	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4713493	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4713494	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6457458	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6901388	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6904848	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6908442	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6919269	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6931599	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7740314	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7751151	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7752735	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7762454	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7766220	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs8180674	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9366788	0.90[AMR][1000 genomes];0.93[EUR][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	nsv1021078	chr6:10819083-11558560	Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv538135	chr6:10819083-11558560	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv432848	chr6:11371614-11560114	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:11405400-11419400	Weak transcription	Aorta	Aorta
2	chr6:11406600-11414600	Weak transcription	Primary B cells from cord blood	blood
3	chr6:11410800-11413400	Enhancers	Primary hematopoietic stem cells short term culture	blood
4	chr6:11410800-11413800	Enhancers	Breast Myoepithelial Primary Cells	Breast
5	chr6:11411000-11415200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr6:11411200-11413800	Enhancers	Primary B cells from peripheral blood	blood
7	chr6:11411200-11413800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
8	chr6:11411200-11415000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
9	chr6:11411200-11415000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
10	chr6:11411200-11415600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
11	chr6:11411600-11417000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr6:11412000-11413000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr6:11412000-11413000	Enhancers	Hela-S3	cervix
14	chr6:11412000-11413200	Enhancers	Adipose Nuclei	Adipose
15	chr6:11412000-11414200	Enhancers	Osteobl	bone
16	chr6:11412200-11413200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr6:11412200-11415400	Enhancers	Primary T helper cells PMA-I stimulated	--
18	chr6:11412400-11413000	Enhancers	Dnd41	blood
19	chr6:11412400-11413200	Enhancers	Cortex derived primary cultured neurospheres	brain
20	chr6:11412400-11413200	Enhancers	Fetal Brain Female	brain
21	chr6:11412400-11413800	Enhancers	Spleen	Spleen
22	chr6:11412400-11414200	Flanking Active TSS	GM12878-XiMat	blood
23	chr6:11412400-11414600	Enhancers	A549	lung
24	chr6:11412400-11415200	Enhancers	Primary monocytes fromperipheralblood	blood
25	chr6:11412400-11415200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr6:11412400-11415400	Enhancers	Primary T helper cells fromperipheralblood	blood
27	chr6:11412400-11416400	Weak transcription	Fetal Kidney	kidney
28	chr6:11412600-11413200	Enhancers	Primary T helper naive cells from peripheral blood	blood
29	chr6:11412600-11413400	Weak transcription	Rectal Mucosa Donor 29	rectum
30	chr6:11412600-11413600	Weak transcription	HUVEC	blood vessel
31	chr6:11412600-11413600	Weak transcription	Monocytes-CD14+_RO01746	blood
32	chr6:11412600-11413800	Weak transcription	HepG2	liver
33	chr6:11412600-11414200	Weak transcription	Pancreatic Islets	Pancreatic Islet
34	chr6:11412600-11414400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr6:11412600-11414800	Weak transcription	HUES6 Cell Line	embryonic stem cell
36	chr6:11412600-11416000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr6:11412600-11416200	Weak transcription	Placenta Amnion	Placenta Amnion
38	chr6:11412600-11416400	Weak transcription	NH-A	brain
39	chr6:11412600-11425600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr6:11412600-11425600	Weak transcription	NHLF	lung
41	chr6:11412800-11414200	Weak transcription	Muscle Satellite Cultured Cells	--
42	chr6:11412800-11414800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr6:11412800-11414800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr6:11412800-11415000	Weak transcription	NHDF-Ad	bronchial
45	chr6:11412800-11415200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr6:11412800-11416400	Weak transcription	HSMM	muscle

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