Variant report

Variant	rs10806098
Chromosome Location	chr6:78176009-78176010
allele	A/G
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	RAD21	chr6:78175670-78176127	H1-hESC	embryonic stem cell:	n/a	chr6:78175859-78175878
2	MAX	chr6:78175846-78176791	GM12878	blood:	n/a	n/a
3	CTCF	chr6:78175726-78176045	GM19238	blood:	n/a	chr6:78175860-78175881 chr6:78175861-78175874
4	ZNF384	chr6:78175881-78176595	GM12878	blood:	n/a	n/a
5	RAD21	chr6:78175566-78176140	HCT-116	colon:	n/a	chr6:78175859-78175878
6	RAD21	chr6:78175596-78176152	H1-hESC	embryonic stem cell:	n/a	chr6:78175859-78175878
7	RAD21	chr6:78175602-78176111	A549	lung:	n/a	chr6:78175859-78175878
8	YY1	chr6:78175763-78176481	SK-N-SH	brain:	n/a	chr6:78176265-78176275
9	TCF7L2	chr6:78175633-78176203	PANC-1	pancreas:	n/a	n/a
10	ZNF143	chr6:78175676-78176730	GM12878	blood:	n/a	chr6:78176069-78176088
11	STAT3	chr6:78175754-78176107	MCF10A-Er-Src	breast:	n/a	chr6:78175936-78175959 chr6:78175934-78175945
12	RUNX3	chr6:78175650-78176511	GM12878	blood:	n/a	chr6:78176123-78176140
13	RAD21	chr6:78175664-78176846	GM12878	blood:	n/a	chr6:78175859-78175878
14	CTCF	chr6:78175696-78176058	HepG2	liver:	n/a	chr6:78175860-78175881 chr6:78175861-78175874
15	RAD21	chr6:78175771-78176040	A549	lung:	n/a	chr6:78175859-78175878
16	TBL1XR1	chr6:78175492-78176028	GM12878	blood:	n/a	n/a
17	WRNIP1	chr6:78175678-78176705	GM12878	blood:	n/a	n/a
18	CTCF	chr6:78175484-78176132	A549	lung:	n/a	chr6:78175860-78175881 chr6:78175861-78175874
19	RAD21	chr6:78175601-78176054	A549	lung:	n/a	chr6:78175859-78175878
20	SPI1	chr6:78175814-78176829	GM12878	blood:	n/a	chr6:78176761-78176770 chr6:78176326-78176339
21	POLR2A	chr6:78175688-78176041	HUVEC	blood vessel:	n/a	n/a
22	CUX1	chr6:78175672-78176091	GM12878	blood:	n/a	n/a
23	RAD21	chr6:78175703-78176051	HepG2	liver:	n/a	chr6:78175859-78175878
24	HDAC2	chr6:78175683-78176045	MCF-7	breast:	n/a	n/a
25	CTCF	chr6:78175552-78176112	HCT-116	colon:	n/a	chr6:78175860-78175881 chr6:78175861-78175874
26	YY1	chr6:78175773-78176430	SK-N-SH_RA	brain:	n/a	chr6:78176265-78176275
27	POLR2A	chr6:78175129-78177168	HUVEC	blood vessel:	n/a	n/a
28	CTCF	chr6:78175633-78176631	IMR90	lung:	n/a	chr6:78175860-78175881 chr6:78175861-78175874
29	BHLHE40	chr6:78175767-78176771	GM12878	blood:	n/a	n/a
30	BCLAF1	chr6:78175799-78176341	GM12878	blood:	n/a	n/a
31	RCOR1	chr6:78175712-78176601	GM12878	blood:	n/a	n/a
32	POLR2A	chr6:78175713-78176090	SK-N-SH	brain:	n/a	n/a
33	ELF1	chr6:78175776-78176599	SK-N-SH	brain:	n/a	chr6:78176326-78176337
34	POLR2A	chr6:78174845-78177075	HUVEC	blood vessel:	n/a	n/a
35	YY1	chr6:78175686-78176093	SK-N-SH_RA	brain:	n/a	n/a
36	POLR2A	chr6:78175968-78176026	MCF10A-Er-Src	breast:	n/a	n/a
37	RAD21	chr6:78175663-78176596	IMR90	lung:	n/a	chr6:78175859-78175878
38	CTCF	chr6:78175621-78176069	H1-hESC	embryonic stem cell:	n/a	chr6:78175860-78175881 chr6:78175861-78175874
39	MYC	chr6:78175758-78176019	MCF10A-Er-Src	breast:	n/a	n/a
40	ZNF143	chr6:78175583-78176986	H1-hESC	embryonic stem cell:	n/a	chr6:78176069-78176088
41	CTCF	chr6:78175722-78176016	Gliobla	brain:	n/a	chr6:78175860-78175881 chr6:78175861-78175874
42	STAT3	chr6:78175765-78176077	MCF10A-Er-Src	breast:	n/a	chr6:78175936-78175959 chr6:78175934-78175945
43	RAD21	chr6:78175668-78176028	SK-N-SH_RA	brain:	n/a	chr6:78175859-78175878
44	RAD21	chr6:78175640-78176061	HepG2	liver:	n/a	chr6:78175859-78175878
45	RAD21	chr6:78175673-78176045	GM12878	blood:	n/a	chr6:78175859-78175878
46	STAT1	chr6:78175781-78176032	GM12878	blood:	n/a	chr6:78175936-78175959
47	YY1	chr6:78175673-78176480	GM12878	blood:	n/a	chr6:78176265-78176275
48	RAD21	chr6:78175586-78176116	H1-hESC	embryonic stem cell:	n/a	chr6:78175859-78175878
49	CTCF	chr6:78175717-78176134	MCF-7	breast:	n/a	chr6:78175860-78175881 chr6:78175861-78175874
50	ELK1	chr6:78175722-78176529	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:78175755..78176369-chr6:78410019..78410778,2	MCF-7	breast:

Variant related genes	Relation type
HTR1B	TF binding region

Extended variants
information (count: 18 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs12662392	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13192352	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2000292	0.80[EUR][1000 genomes]
rs4142329	0.95[CEU][hapmap];0.86[CHD][hapmap];0.88[GIH][hapmap];0.91[JPT][hapmap];0.94[MEX][hapmap];0.94[TSI][hapmap]
rs62416459	0.85[EUR][1000 genomes]
rs6296	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6298	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6916063	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.85[YRI][hapmap]
rs6920728	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1017082	chr6:77585310-78258237	Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv534282	chr6:77764575-78351994	Weak transcription Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv1034979	chr6:77781244-78426249	Active TSS Weak transcription ZNF genes & repeats Enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv538324	chr6:77781244-78426249	Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv1015307	chr6:77902559-78352291	Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv1028259	chr6:78059491-78709871	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv538325	chr6:78059491-78709871	Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	esv2758062	chr6:78100020-78283042	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	esv2759445	chr6:78100020-78283042	Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10806098	IRAK1BP1	cis	parietal	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:78174200-78176800	Flanking Active TSS	HUVEC	blood vessel
2	chr6:78174600-78176400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr6:78175000-78176200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr6:78175400-78176200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr6:78175400-78176600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr6:78175400-78177000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
7	chr6:78175400-78177200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
8	chr6:78175400-78177200	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
9	chr6:78175600-78176200	Flanking Bivalent TSS/Enh	Primary T helper cells fromperipheralblood	blood
10	chr6:78175600-78176200	Bivalent/Poised TSS	Primary T killer memory cells from peripheral blood	blood
11	chr6:78175600-78176200	Bivalent/Poised TSS	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr6:78175600-78176200	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
13	chr6:78175600-78176400	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
14	chr6:78175600-78176400	Active TSS	A549	lung
15	chr6:78175600-78176600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells short term culture	blood
16	chr6:78175600-78176600	Flanking Bivalent TSS/Enh	Brain Angular Gyrus	brain
17	chr6:78175600-78176800	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
18	chr6:78175600-78176800	Bivalent/Poised TSS	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr6:78175600-78176800	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
20	chr6:78175600-78176800	Bivalent/Poised TSS	Primary B cells from cord blood	blood
21	chr6:78175600-78176800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr6:78175600-78176800	Flanking Bivalent TSS/Enh	Primary Natural Killer cells fromperipheralblood	blood
23	chr6:78175600-78176800	Active TSS	Aorta	Aorta
24	chr6:78175600-78176800	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
25	chr6:78175600-78176800	Active TSS	Fetal Heart	heart
26	chr6:78175600-78176800	Bivalent/Poised TSS	Fetal Kidney	kidney
27	chr6:78175600-78176800	Active TSS	Ovary	ovary
28	chr6:78175600-78176800	Active TSS	GM12878-XiMat	blood
29	chr6:78175600-78177000	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
30	chr6:78175600-78177000	Bivalent/Poised TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr6:78175600-78177000	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr6:78175600-78177000	Bivalent/Poised TSS	Primary T cells from cord blood	blood
33	chr6:78175600-78177000	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
34	chr6:78175600-78177000	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain
35	chr6:78175600-78177000	Bivalent/Poised TSS	Duodenum Mucosa	Duodenum
36	chr6:78175600-78177000	Active TSS	Pancreatic Islets	Pancreatic Islet
37	chr6:78175600-78177000	Active TSS	Right Ventricle	heart
38	chr6:78175600-78177200	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr6:78175800-78176200	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr6:78175800-78176200	Bivalent/Poised TSS	Primary neutrophils fromperipheralblood	blood
41	chr6:78175800-78176200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr6:78175800-78176200	Flanking Bivalent TSS/Enh	Brain Cingulate Gyrus	brain
43	chr6:78175800-78176200	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
44	chr6:78175800-78176200	Active TSS	HMEC	breast
45	chr6:78175800-78176400	Bivalent/Poised TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr6:78175800-78176400	Bivalent/Poised TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr6:78175800-78176400	Active TSS	Muscle Satellite Cultured Cells	--
48	chr6:78175800-78176400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr6:78175800-78176400	Bivalent/Poised TSS	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr6:78175800-78176400	Bivalent/Poised TSS	Brain Anterior Caudate	brain

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