Variant report

Variant	rs6930989
Chromosome Location	chr6:149354847-149354848
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	EP300	chr6:149353633-149354949	GM12878	blood:	n/a	chr6:149354049-149354063
2	BHLHE40	chr6:149353074-149354942	GM12878	blood:	n/a	chr6:149353322-149353338
3	MEF2A	chr6:149353574-149355007	GM12878	blood:	n/a	chr6:149354238-149354253 chr6:149354482-149354496
4	RCOR1	chr6:149352928-149355080	GM12878	blood:	n/a	n/a
5	FOXM1	chr6:149353279-149355039	GM12878	blood:	n/a	n/a
6	RUNX3	chr6:149353036-149354920	GM12878	blood:	n/a	n/a
7	RUNX3	chr6:149352788-149355044	GM12878	blood:	n/a	n/a
8	NFIC	chr6:149353446-149354966	GM12878	blood:	n/a	chr6:149354369-149354386 chr6:149354369-149354385
9	STAT5A	chr6:149352729-149354965	GM12878	blood:	n/a	chr6:149353461-149353469 chr6:149352925-149352937 chr6:149354815-149354827 chr6:149353941-149353950
10	POLR2A	chr6:149354765-149354910	GM12878	blood:	n/a	n/a
11	RELA	chr6:149353445-149354947	GM12891	blood:	n/a	n/a
12	RELA	chr6:149353750-149354932	GM10847	blood:	n/a	n/a
13	RELA	chr6:149353700-149354944	GM12878	blood:	n/a	n/a
14	MAX	chr6:149353554-149355033	GM12878	blood:	n/a	n/a
15	NFIC	chr6:149353866-149354862	HepG2	liver:	n/a	chr6:149354369-149354386 chr6:149354369-149354385
16	MAX	chr6:149354627-149355087	A549	lung:	n/a	n/a
17	STAT5A	chr6:149353481-149354933	GM12878	blood:	n/a	chr6:149354815-149354827 chr6:149353941-149353950
18	USF2	chr6:149354380-149354927	GM12878	blood:	n/a	n/a
19	MAZ	chr6:149352859-149355036	GM12878	blood:	n/a	n/a
20	MAX	chr6:149352872-149355087	A549	lung:	n/a	n/a
21	TBL1XR1	chr6:149353044-149354932	GM12878	blood:	n/a	n/a
22	EP300	chr6:149353199-149354968	GM12878	blood:	n/a	chr6:149354049-149354063
23	ATF2	chr6:149353119-149355078	GM12878	blood:	n/a	n/a
24	POLR2A	chr6:149354555-149354967	GM12878	blood:	n/a	n/a
25	CHD1	chr6:149351910-149354871	GM12878	blood:	n/a	chr6:149354817-149354827
26	BCLAF1	chr6:149353433-149354953	GM12878	blood:	n/a	chr6:149353941-149353950
27	TBP	chr6:149351784-149355037	GM12878	blood:	n/a	n/a
28	POLR2A	chr6:149352295-149354997	GM12878	blood:	n/a	n/a
29	CEBPB	chr6:149353296-149355022	GM12878	blood:	n/a	n/a
30	RELA	chr6:149353502-149354923	GM18951	blood:	n/a	n/a
31	ATF2	chr6:149353613-149354994	GM12878	blood:	n/a	n/a
32	NFIC	chr6:149352353-149355278	GM12878	blood:	n/a	chr6:149354369-149354386 chr6:149354369-149354385
33	MTA3	chr6:149352755-149354956	GM12878	blood:	n/a	n/a
34	IRF4	chr6:149354553-149354867	GM12878	blood:	n/a	n/a
35	MEF2A	chr6:149353537-149354891	GM12878	blood:	n/a	chr6:149354238-149354253 chr6:149354482-149354496
36	BCL11A	chr6:149354611-149354883	GM12878	blood:	n/a	n/a
37	BCL3	chr6:149353106-149354948	GM12878	blood:	n/a	chr6:149353941-149353950
38	PML	chr6:149352714-149355084	GM12878	blood:	n/a	n/a
39	BATF	chr6:149354522-149354910	GM12878	blood:	n/a	n/a
40	TCF12	chr6:149352529-149354883	A549	lung:	n/a	chr6:149353533-149353543
41	CUX1	chr6:149353603-149355079	GM12878	blood:	n/a	n/a
42	RELA	chr6:149353796-149354906	GM12892	blood:	n/a	n/a
43	BCL11A	chr6:149354529-149354881	GM12878	blood:	n/a	n/a
44	TEAD4	chr6:149353691-149354883	HepG2	liver:	n/a	n/a
45	BATF	chr6:149354511-149354909	GM12878	blood:	n/a	n/a
46	RELA	chr6:149353747-149354898	GM19099	blood:	n/a	n/a
47	CHD2	chr6:149353000-149354907	GM12878	blood:	n/a	chr6:149354817-149354827
48	IKZF1	chr6:149353264-149354893	GM12878	blood:	n/a	n/a
49	RELA	chr6:149353736-149354992	GM19193	blood:	n/a	n/a
50	EBF1	chr6:149352960-149355028	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:149351823..149355344-chr6:149638842..149641991,4	MCF-7	breast:
2	chr6:149352653..149356079-chr6:149835245..149838856,4	MCF-7	breast:
3	chr6:149353980..149354853-chr6:149401096..149401673,2	MCF-7	breast:
4	chr6:149353960..149356786-chr6:149766378..149768113,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000236591	TF binding region
ENSG00000252244	Chromatin interaction
ENSG00000055208	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10457074	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2275423	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2340751	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2340752	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2340801	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2340802	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2879843	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4318907	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4377808	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4897074	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4897076	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6570920	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6904550	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6931744	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6936176	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7747463	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7748978	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7765778	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7774457	0.81[EUR][1000 genomes]
rs7774887	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9377187	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9377188	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9399678	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1032690	chr6:149206106-149398712	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
2	nsv1032319	chr6:149271433-149550525	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv538470	chr6:149271433-149550525	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	nsv830842	chr6:149272321-149427340	Enhancers Bivalent Enhancer ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:149305400-149381400	Weak transcription	Gastric	stomach
2	chr6:149336200-149358000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr6:149337600-149358000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr6:149339400-149364600	Weak transcription	Lung	lung
5	chr6:149341000-149365400	Weak transcription	Right Ventricle	heart
6	chr6:149343200-149358000	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr6:149344000-149357200	Weak transcription	Fetal Muscle Trunk	muscle
8	chr6:149344000-149357400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr6:149344600-149357800	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr6:149344800-149358000	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr6:149345000-149355200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr6:149345400-149362000	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr6:149345600-149355000	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr6:149345600-149358000	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr6:149347800-149356800	Weak transcription	Fetal Muscle Leg	muscle
16	chr6:149348000-149367400	Weak transcription	Primary B cells from cord blood	blood
17	chr6:149350200-149357600	Weak transcription	Colon Smooth Muscle	Colon
18	chr6:149350400-149358000	Weak transcription	Fetal Kidney	kidney
19	chr6:149351800-149355000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr6:149351800-149355400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr6:149352400-149355200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr6:149352400-149355200	Enhancers	Primary hematopoietic stem cells short term culture	blood
23	chr6:149352400-149355600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr6:149352600-149355200	Enhancers	Breast Myoepithelial Primary Cells	Breast
25	chr6:149352800-149355000	Enhancers	Primary hematopoietic stem cells	blood
26	chr6:149352800-149355000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr6:149352800-149355600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
28	chr6:149352800-149355800	Enhancers	Fetal Lung	lung
29	chr6:149353000-149355200	Enhancers	NHDF-Ad	bronchial
30	chr6:149353000-149355800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr6:149353000-149355800	Enhancers	Ovary	ovary
32	chr6:149353400-149355000	Enhancers	Brain Anterior Caudate	brain
33	chr6:149353400-149355000	Flanking Active TSS	A549	lung
34	chr6:149353400-149355800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr6:149353600-149355400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
36	chr6:149353600-149357200	Weak transcription	HUES6 Cell Line	embryonic stem cell
37	chr6:149353800-149355000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr6:149353800-149355800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
39	chr6:149353800-149356000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr6:149353800-149356000	Enhancers	Dnd41	blood
41	chr6:149353800-149356800	Weak transcription	Fetal Stomach	stomach
42	chr6:149353800-149357200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr6:149353800-149357400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr6:149353800-149358000	Enhancers	HSMMtube	muscle
45	chr6:149353800-149362400	Weak transcription	Pancreas	Pancrea
46	chr6:149353800-149367400	Weak transcription	Spleen	Spleen
47	chr6:149353800-149367800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr6:149353800-149369800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr6:149354000-149355000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr6:149354000-149355000	Enhancers	Aorta	Aorta

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