Variant report

Variant	rs1413967
Chromosome Location	chr6:79789012-79789013
allele	A/C
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	CHD1	chr6:79787731-79789080	GM12878	blood:	n/a	n/a
2	POLR2A	chr6:79787424-79789088	K562	blood:	n/a	n/a
3	POLR2A	chr6:79787516-79789700	MCF10A-Er-Src	breast:	n/a	n/a
4	REST	chr6:79787366-79789182	H1-neurons	neurons:	n/a	n/a
5	CHD1	chr6:79788268-79789641	H1-hESC	embryonic stem cell:	n/a	n/a
6	MYC	chr6:79787925-79789050	MCF10A-Er-Src	breast:	n/a	chr6:79788121-79788130 chr6:79788261-79788271 chr6:79788548-79788558
7	MAZ	chr6:79787680-79789041	HepG2	liver:	n/a	chr6:79788121-79788130 chr6:79788261-79788271
8	RELA	chr6:79787742-79789103	GM12878	blood:	n/a	n/a
9	TBP	chr6:79787785-79789763	Hela-S3	cervix:	n/a	n/a
10	POLR2A	chr6:79787611-79789770	PBDE	blood:	n/a	n/a
11	TBP	chr6:79787571-79789117	K562	blood:	n/a	n/a
12	CUX1	chr6:79788275-79789121	GM12878	blood:	n/a	n/a
13	GATA1	chr6:79787758-79789022	PBDE	blood:	n/a	chr6:79788942-79788952
14	POLR2A	chr6:79786522-79789159	K562	blood:	n/a	n/a
15	IRF1	chr6:79787694-79789931	K562	blood:	n/a	n/a
16	RELA	chr6:79787747-79789038	GM10847	blood:	n/a	n/a
17	MAZ	chr6:79787567-79789186	GM12878	blood:	n/a	chr6:79788121-79788130 chr6:79788261-79788271
18	MAX	chr6:79787742-79789121	Hela-S3	cervix:	n/a	chr6:79788121-79788130 chr6:79788261-79788271 chr6:79788548-79788558
19	SIN3A	chr6:79786155-79789041	H1-hESC	embryonic stem cell:	n/a	chr6:79788341-79788350
20	CEBPB	chr6:79788058-79789156	K562	blood:	n/a	n/a
21	TBP	chr6:79787765-79789047	HepG2	liver:	n/a	n/a
22	RELA	chr6:79787753-79789030	GM19099	blood:	n/a	n/a
23	ARID3A	chr6:79787796-79789130	HepG2	liver:	n/a	n/a
24	MXI1	chr6:79785662-79789451	SK-N-SH	brain:	n/a	n/a
25	POLR2A	chr6:79787527-79789180	MCF10A-Er-Src	breast:	n/a	n/a
26	MAFK	chr6:79788299-79789258	K562	blood:	n/a	n/a
27	POLR2A	chr6:79787273-79789122	H1-hESC	embryonic stem cell:	n/a	n/a
28	TBL1XR1	chr6:79787730-79789686	GM12878	blood:	n/a	n/a
29	ARID3A	chr6:79787980-79790015	K562	blood:	n/a	n/a
30	IRF1	chr6:79787687-79789209	K562	blood:	n/a	n/a
31	RFX5	chr6:79787709-79789702	Hela-S3	cervix:	n/a	n/a
32	KAP1	chr6:79787845-79789144	U2OS	brain:	n/a	chr6:79788235-79788243
33	CUX1	chr6:79788188-79789529	K562	blood:	n/a	n/a
34	POLR2A	chr6:79787577-79789138	GM12891	blood:	n/a	n/a
35	POLR2A	chr6:79786537-79789027	Raji	blood:	n/a	n/a
36	POLR2A	chr6:79787541-79789080	K562	blood:	n/a	n/a
37	POLR2A	chr6:79786466-79789094	GM19099	blood:	n/a	n/a
38	KAP1	chr6:79787894-79789028	HEK293	kidney:	n/a	chr6:79788235-79788243

No.	Distal block	Cell Line	Cell type
1	chr6:79786974..79789353-chr6:80246033..80249654,3	K562	blood:
2	chr6:79782683..79789958-chr6:79939846..79945776,22	MCF-7	breast:
3	chr6:79788686..79790517-chr6:80354906..80356790,2	K562	blood:
4	chr6:79785425..79789135-chr6:79942833..79950296,12	MCF-7	breast:
5	chr6:79785468..79790645-chr6:79941426..79946271,8	K562	blood:
6	chr6:79762969..79765630-chr6:79788155..79789824,2	MCF-7	breast:
7	chr6:79787878..79790499-chr6:79943656..79946271,3	K562	blood:
8	chr6:79575800..79578597-chr6:79786334..79789260,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-IRAK1BP1-3	chr6:79787562-79790141	NONHSAT113677

Variant related genes	Relation type
PHIP	TF binding region
ENSG00000270362	Chromatin interaction
ENSG00000118418	Chromatin interaction
ENSG00000135338	Chromatin interaction
ENSG00000146243	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs12529043	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs1415861	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.88[AMR][1000 genomes]
rs1415862	0.87[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes]
rs1415863	0.86[ASW][hapmap];1.00[CEU][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1538234	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1890230	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs28811946	0.97[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4547969	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4706748	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4706749	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs56118785	1.00[AMR][1000 genomes]
rs58047896	0.97[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6454094	1.00[ASW][hapmap];0.86[CEU][hapmap];1.00[GIH][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6454095	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6900076	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6906655	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6916942	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6918296	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6929315	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6940635	1.00[CEU][hapmap];0.90[YRI][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6941107	0.97[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs73764089	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7739298	0.86[ASW][hapmap];1.00[CEU][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7747479	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7756903	0.87[CEU][hapmap];0.91[YRI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7758407	0.97[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7775074	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7776322	0.97[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9343862	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9361485	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830705	chr6:79659297-79829530	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
2	nsv518477	chr6:79700159-79850427	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:79783800-79790600	Active TSS	K562	blood
2	chr6:79784000-79789800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr6:79784000-79789800	Active TSS	iPS-20b Cell Line	embryonic stem cell
4	chr6:79784400-79789400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr6:79784400-79789600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr6:79784600-79789800	Active TSS	Fetal Brain Female	brain
7	chr6:79784800-79789400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
8	chr6:79784800-79789600	Active TSS	H1 Cell Line	embryonic stem cell
9	chr6:79785000-79789200	Active TSS	Breast Myoepithelial Primary Cells	Breast
10	chr6:79785000-79789200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr6:79785000-79789400	Active TSS	A549	lung
12	chr6:79785000-79789600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr6:79785000-79789800	Active TSS	Right Atrium	heart
14	chr6:79785200-79789200	Active TSS	HMEC	breast
15	chr6:79785200-79789400	Active TSS	iPS-15b Cell Line	embryonic stem cell
16	chr6:79785200-79789600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr6:79785200-79789800	Active TSS	ES-I3 Cell Line	embryonic stem cell
18	chr6:79785200-79790000	Active TSS	HUES6 Cell Line	embryonic stem cell
19	chr6:79785400-79789200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr6:79785400-79789200	Active TSS	Aorta	Aorta
21	chr6:79785400-79789600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr6:79785400-79789600	Active TSS	Psoas Muscle	Psoas
23	chr6:79785400-79789800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr6:79785400-79789800	Active TSS	Right Ventricle	heart
25	chr6:79785400-79789800	Active TSS	Thymus	Thymus
26	chr6:79785600-79789200	Active TSS	Primary T cells fromperipheralblood	blood
27	chr6:79785600-79789200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr6:79785600-79789200	Active TSS	Colonic Mucosa	Colon
29	chr6:79785600-79789200	Active TSS	Fetal Intestine Large	intestine
30	chr6:79785600-79789200	Active TSS	Stomach Smooth Muscle	stomach
31	chr6:79785600-79789400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr6:79785600-79789400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
33	chr6:79785600-79789400	Active TSS	Duodenum Smooth Muscle	Duodenum
34	chr6:79785600-79789400	Active TSS	Pancreatic Islets	Pancreatic Islet
35	chr6:79785600-79789400	Active TSS	Fetal Stomach	stomach
36	chr6:79785600-79789400	Active TSS	GM12878-XiMat	blood
37	chr6:79785600-79789400	Active TSS	Hela-S3	cervix
38	chr6:79785600-79789600	Active TSS	Fetal Thymus	thymus
39	chr6:79785600-79789600	Active TSS	NHDF-Ad	bronchial
40	chr6:79785800-79789200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
41	chr6:79785800-79789200	Active TSS	iPS-18 Cell Line	embryonic stem cell
42	chr6:79785800-79789200	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
43	chr6:79785800-79789200	Active TSS	Fetal Muscle Trunk	muscle
44	chr6:79785800-79789200	Active TSS	Ovary	ovary
45	chr6:79785800-79789400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr6:79785800-79789400	Active TSS	Fetal Intestine Small	intestine
47	chr6:79785800-79789400	Active TSS	Osteobl	bone
48	chr6:79785800-79789600	Active TSS	Fetal Muscle Leg	muscle
49	chr6:79786000-79789200	Active TSS	H9 Cell Line	embryonic stem cell
50	chr6:79786000-79789200	Active TSS	Brain Substantia Nigra	brain

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