Variant report

Variant	rs1778258
Chromosome Location	chr6:78174209-78174210
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:38)
CpG islands
(count:0)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:38 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAX	chr6:78173562-78174257	ECC-1	luminal epithelium:	n/a	n/a
2	TCF12	chr6:78173934-78174255	H1-hESC	embryonic stem cell:	n/a	chr6:78173954-78173964
3	POLR2A	chr6:78173703-78174257	H1-hESC	embryonic stem cell:	n/a	n/a
4	MAX	chr6:78172404-78174410	H1-hESC	embryonic stem cell:	n/a	n/a
5	RAD21	chr6:78173680-78174374	H1-hESC	embryonic stem cell:	n/a	chr6:78173779-78173792
6	FOSL1	chr6:78173940-78174426	H1-hESC	embryonic stem cell:	n/a	n/a
7	SIN3A	chr6:78171981-78174406	H1-hESC	embryonic stem cell:	n/a	chr6:78174234-78174243
8	MAX	chr6:78173694-78174323	H1-hESC	embryonic stem cell:	n/a	n/a
9	YY1	chr6:78173854-78174386	H1-hESC	embryonic stem cell:	n/a	n/a
10	E2F6	chr6:78173555-78174405	H1-hESC	embryonic stem cell:	n/a	chr6:78173843-78173852
11	TBP	chr6:78173875-78174360	H1-hESC	embryonic stem cell:	n/a	n/a
12	EGR1	chr6:78173903-78174416	H1-hESC	embryonic stem cell:	n/a	n/a
13	JUND	chr6:78174076-78174232	H1-hESC	embryonic stem cell:	n/a	n/a
14	GTF2F1	chr6:78173953-78174301	H1-hESC	embryonic stem cell:	n/a	n/a
15	CTBP2	chr6:78171789-78174500	H1-hESC	embryonic stem cell:	n/a	n/a
16	EGR1	chr6:78173810-78174409	H1-hESC	embryonic stem cell:	n/a	n/a
17	POLR2A	chr6:78172052-78174487	PANC-1	pancreas:	n/a	n/a
18	TEAD4	chr6:78173953-78174289	H1-hESC	embryonic stem cell:	n/a	n/a
19	CHD2	chr6:78173857-78174370	H1-hESC	embryonic stem cell:	n/a	n/a
20	POLR2A	chr6:78171374-78174685	HUVEC	blood vessel:	n/a	n/a
21	ZNF143	chr6:78173756-78174565	H1-hESC	embryonic stem cell:	n/a	n/a
22	SIN3AK20	chr6:78173904-78174344	H1-hESC	embryonic stem cell:	n/a	n/a
23	POLR2A	chr6:78170850-78175058	HUVEC	blood vessel:	n/a	n/a
24	SP1	chr6:78173847-78174289	H1-hESC	embryonic stem cell:	n/a	chr6:78174193-78174207
25	RXRA	chr6:78174027-78174273	H1-hESC	embryonic stem cell:	n/a	n/a
26	EP300	chr6:78173931-78174396	H1-hESC	embryonic stem cell:	n/a	n/a
27	ZNF143	chr6:78174132-78174301	GM12878	blood:	n/a	n/a
28	E2F6	chr6:78172660-78174411	H1-hESC	embryonic stem cell:	n/a	chr6:78173843-78173852
29	POLR2A	chr6:78171260-78177131	HUVEC	blood vessel:	n/a	n/a
30	POLR2A	chr6:78173740-78174293	H1-neurons	neurons:	n/a	n/a
31	POLR2A	chr6:78171285-78174701	HUVEC	blood vessel:	n/a	n/a
32	TEAD4	chr6:78173866-78174290	H1-hESC	embryonic stem cell:	n/a	n/a
33	POLR2A	chr6:78172021-78174538	HUVEC	blood vessel:	n/a	n/a
34	MXI1	chr6:78173910-78174313	H1-hESC	embryonic stem cell:	n/a	n/a
35	YY1	chr6:78173911-78174355	H1-hESC	embryonic stem cell:	n/a	n/a
36	POLR2A	chr6:78173682-78174500	PANC-1	pancreas:	n/a	n/a
37	FOSL1	chr6:78173927-78174425	H1-hESC	embryonic stem cell:	n/a	n/a
38	MYC	chr6:78173906-78174220	H1-hESC	embryonic stem cell:	n/a	n/a

No data

Variant related genes	Relation type
HTR1B	TF binding region

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs12173930	0.85[EUR][1000 genomes]
rs1343488	1.00[CEU][hapmap]
rs62416431	0.85[ASN][1000 genomes]
rs6297	0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7748725	1.00[CEU][hapmap]
rs9352485	1.00[CEU][hapmap]
rs9361238	0.90[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

No data

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:78169400-78174600	Active TSS	Aorta	Aorta
2	chr6:78171400-78174400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr6:78171400-78174600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
4	chr6:78171400-78174600	Bivalent/Poised TSS	Brain Anterior Caudate	brain
5	chr6:78171600-78174400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr6:78171600-78174600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
7	chr6:78171800-78174400	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
8	chr6:78171800-78174400	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
9	chr6:78171800-78174800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
10	chr6:78171800-78174800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
11	chr6:78172000-78174400	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
12	chr6:78172200-78174400	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr6:78172200-78174400	Bivalent/Poised TSS	ES-UCSF4 Cell Line	embryonic stem cell
14	chr6:78172200-78174400	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr6:78172200-78174400	Bivalent/Poised TSS	Pancreatic Islets	Pancreatic Islet
16	chr6:78172200-78174400	Bivalent/Poised TSS	Osteobl	bone
17	chr6:78172200-78174600	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
18	chr6:78172400-78174400	Flanking Bivalent TSS/Enh	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr6:78172400-78174400	Flanking Bivalent TSS/Enh	Brain Cingulate Gyrus	brain
20	chr6:78172400-78174400	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
21	chr6:78172400-78174400	Flanking Bivalent TSS/Enh	Duodenum Smooth Muscle	Duodenum
22	chr6:78172400-78174400	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
23	chr6:78172400-78174400	Bivalent Enhancer	Spleen	Spleen
24	chr6:78172400-78174600	Bivalent/Poised TSS	Placenta	Placenta
25	chr6:78172400-78174600	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
26	chr6:78172600-78174400	Flanking Active TSS	HMEC	breast
27	chr6:78172600-78174400	Flanking Bivalent TSS/Enh	NHEK	skin
28	chr6:78172600-78174600	Flanking Bivalent TSS/Enh	Brain Hippocampus Middle	brain
29	chr6:78172800-78174400	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
30	chr6:78173000-78174600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
31	chr6:78173000-78174600	Active TSS	H9 Cell Line	embryonic stem cell
32	chr6:78173000-78174800	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr6:78173200-78174400	Bivalent/Poised TSS	A549	lung
34	chr6:78173200-78174400	Bivalent/Poised TSS	NHLF	lung
35	chr6:78173400-78174400	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr6:78173400-78174400	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr6:78173400-78174400	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr6:78173400-78174600	Bivalent/Poised TSS	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr6:78173600-78174400	Flanking Bivalent TSS/Enh	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr6:78173600-78174600	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr6:78173600-78174600	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain
42	chr6:78173600-78175600	Bivalent Enhancer	Fetal Brain Male	brain
43	chr6:78173800-78174400	Bivalent/Poised TSS	Esophagus	oesophagus
44	chr6:78173800-78174600	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr6:78174000-78174400	Flanking Bivalent TSS/Enh	Breast Myoepithelial Primary Cells	Breast
46	chr6:78174000-78174400	Bivalent/Poised TSS	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr6:78174000-78174400	Flanking Bivalent TSS/Enh	Fetal Intestine Small	intestine
48	chr6:78174000-78174400	Bivalent/Poised TSS	Fetal Kidney	kidney
49	chr6:78174000-78174600	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
50	chr6:78174000-78175000	Bivalent/Poised TSS	Primary hematopoietic stem cells	blood

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