Variant report

Variant	rs1213366
Chromosome Location	chr6:78176870-78176871
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:14)
CpG islands
(count:61)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:14 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr6:78176780-78176930	AoAF	blood vessel:	n/a	n/a
2	CTCF	chr6:78176740-78176890	AG04450	lung:	n/a	n/a
3	POLR2A	chr6:78175129-78177168	HUVEC	blood vessel:	n/a	n/a
4	CTCF	chr6:78176720-78176870	HPAF	blood vessel:	n/a	n/a
5	CHD2	chr6:78176191-78176975	H1-hESC	embryonic stem cell:	n/a	n/a
6	POLR2A	chr6:78174845-78177075	HUVEC	blood vessel:	n/a	n/a
7	CTCF	chr6:78176740-78176890	HVMF	connective:	n/a	n/a
8	ZNF143	chr6:78175583-78176986	H1-hESC	embryonic stem cell:	n/a	chr6:78176069-78176088
9	POLR2A	chr6:78174772-78177031	HUVEC	blood vessel:	n/a	n/a
10	SIN3A	chr6:78175645-78176936	H1-hESC	embryonic stem cell:	n/a	n/a
11	CTCF	chr6:78176800-78176950	SK-N-SH_RA	brain:	n/a	n/a
12	POLR2A	chr6:78171260-78177131	HUVEC	blood vessel:	n/a	n/a
13	CTCF	chr6:78176760-78176910	HVMF	connective:	n/a	n/a
14	CTBP2	chr6:78175660-78177142	H1-hESC	embryonic stem cell:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr6:78176847-78176897	HIPEpiC	eye:	n/a
2	chr6:78176847-78176897	NB4	blood:	n/a
3	chr6:78176847-78176897	HEEpiC	esophagus:	n/a
4	chr6:78176847-78176897	HPAEpiC	pulmonary alveolar:	n/a
5	chr6:78176847-78176897	T-47D	breast:	n/a
6	chr6:78176847-78176897	K562	blood:	n/a
7	chr6:78176847-78176897	GM12891	blood:	n/a
8	chr6:78176847-78176897	AoSMC	blood vessel:	n/a
9	chr6:78176847-78176897	Hela-S3	cervix:	n/a
10	chr6:78176847-78176897	H1-hESC	embryonic stem cell:	embryo
11	chr6:78176847-78176897	HCF	heart:	n/a
12	chr6:78176847-78176897	NHDF-neo	bronchial:	n/a
13	chr6:78176847-78176897	BJ	skin:	n/a
14	chr6:78176847-78176897	PrEC	prostate:	n/a
15	chr6:78176847-78176897	U87	brain:	n/a
16	chr6:78176847-78176897	HEK293	kidney:	embryo
17	chr6:78176847-78176897	PANC-1	pancreas:	n/a
18	chr6:78176847-78176897	IMR90	lung:	fetal
19	chr6:78176847-78176897	NHBE	bronchial:	n/a
20	chr6:78176847-78176897	LNCaP	prostate:	n/a
21	chr6:78176847-78176897	A549	lung:	n/a
22	chr6:78176847-78176897	HRE	kidney:	n/a
23	chr6:78176847-78176897	HepG2	liver:	n/a
24	chr6:78176847-78176897	ProgFib	skin:	n/a
25	chr6:78176847-78176897	MCF10A-Er-Src	breast:	n/a
26	chr6:78176847-78176897	GM19239	blood:	n/a
27	chr6:78176847-78176897	HCPEpiC	choroid plexus:	n/a
28	chr6:78176847-78176897	HAEpiC	amniotic membrane:	n/a
29	chr6:78176847-78176897	Hepatocyte	liver:	n/a
30	chr6:78176847-78176897	HRPEpiC	eye:	n/a
31	chr6:78176847-78176897	HCT-116	colon:	n/a
32	chr6:78176847-78176897	ovcar-3	ovarian:	n/a
33	chr6:78176847-78176897	HRCEpiC	kidney:	n/a
34	chr6:78176847-78176897	RPTEC	kidney:	n/a
35	chr6:78176847-78176897	HCM	heart:	n/a
36	chr6:78176847-78176897	HL-60	blood:	n/a
37	chr6:78176847-78176897	SK-N-SH_RA	brain:	n/a
38	chr6:78176847-78176897	NT2-D1	testis:	n/a
39	chr6:78176847-78176897	PFSK-1	brain:	n/a
40	chr6:78176847-78176897	AG09309	skin:	n/a
41	chr6:78176847-78176897	AG10803	skin:	n/a
42	chr6:78176847-78176897	HMEC	breast:	n/a
43	chr6:78176847-78176897	SAEC	small airway:	n/a
44	chr6:78176847-78176897	GM12878	blood:	n/a
45	chr6:78176847-78176897	Caco-2	colon:	n/a
46	chr6:78176847-78176897	ECC-1	luminal epithelium:	n/a
47	chr6:78176847-78176897	AG09319	gingival:	n/a
48	chr6:78176847-78176897	SK-N-SH	brain:	n/a
49	chr6:78176847-78176897	HNPCEpiC	eye:	n/a
50	chr6:78176847-78176897	MCF-7	breast:	n/a

No data

Variant related genes	Relation type
HTR1B	TF binding region
HTR1B	CpG island

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs11568817	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1213356	0.85[CHB][hapmap];0.91[CHD][hapmap]
rs1213357	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs1213369	1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs1213371	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1213373	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1228814	0.85[CEU][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs130058	0.82[JPT][hapmap]
rs1361847	0.85[CHB][hapmap]
rs17273700	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56088227	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9361233	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9361234	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9361235	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][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

No data

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:78175400-78177000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
2	chr6:78175400-78177200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
3	chr6:78175400-78177200	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
4	chr6:78175600-78177000	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
5	chr6:78175600-78177000	Bivalent/Poised TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr6:78175600-78177000	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr6:78175600-78177000	Bivalent/Poised TSS	Primary T cells from cord blood	blood
8	chr6:78175600-78177000	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
9	chr6:78175600-78177000	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain
10	chr6:78175600-78177000	Bivalent/Poised TSS	Duodenum Mucosa	Duodenum
11	chr6:78175600-78177000	Active TSS	Pancreatic Islets	Pancreatic Islet
12	chr6:78175600-78177000	Active TSS	Right Ventricle	heart
13	chr6:78175600-78177200	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr6:78175800-78177000	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr6:78175800-78177000	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr6:78175800-78177000	Active TSS	Primary T helper naive cells from peripheral blood	blood
17	chr6:78175800-78177000	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
18	chr6:78175800-78177000	Bivalent/Poised TSS	Colonic Mucosa	Colon
19	chr6:78175800-78177000	Active TSS	Colon Smooth Muscle	Colon
20	chr6:78175800-78177000	Flanking Bivalent TSS/Enh	Fetal Brain Female	brain
21	chr6:78175800-78177000	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
22	chr6:78175800-78177000	Active TSS	Stomach Mucosa	stomach
23	chr6:78175800-78177000	Active TSS	NHLF	lung
24	chr6:78175800-78177200	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
25	chr6:78175800-78177200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
26	chr6:78176000-78177000	Bivalent/Poised TSS	Primary T helper cells PMA-I stimulated	--
27	chr6:78176000-78177000	Bivalent/Poised TSS	Brain Germinal Matrix	brain
28	chr6:78176000-78177000	Flanking Bivalent TSS/Enh	Brain Hippocampus Middle	brain
29	chr6:78176200-78177000	Flanking Active TSS	HMEC	breast
30	chr6:78176400-78177000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
31	chr6:78176400-78177000	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr6:78176400-78177000	Flanking Bivalent TSS/Enh	Brain Anterior Caudate	brain
33	chr6:78176400-78177000	Active TSS	Duodenum Smooth Muscle	Duodenum
34	chr6:78176400-78177200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr6:78176400-78177200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr6:78176400-78177200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr6:78176400-78177200	Flanking Active TSS	NH-A	brain
38	chr6:78176400-78177200	Flanking Active TSS	NHEK	skin
39	chr6:78176400-78177400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr6:78176600-78177000	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
41	chr6:78176600-78177000	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
42	chr6:78176600-78177000	Bivalent/Poised TSS	Primary T killer memory cells from peripheral blood	blood
43	chr6:78176600-78177000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr6:78176600-78177000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
45	chr6:78176600-78177000	Bivalent/Poised TSS	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr6:78176600-78177000	Flanking Active TSS	Brain Angular Gyrus	brain
47	chr6:78176600-78177000	Flanking Active TSS	Brain Substantia Nigra	brain
48	chr6:78176600-78177000	Bivalent Enhancer	Psoas Muscle	Psoas
49	chr6:78176600-78177000	Bivalent/Poised TSS	Stomach Smooth Muscle	stomach
50	chr6:78176600-78177200	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell

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