Variant report

Variant	rs6678608
Chromosome Location	chr1:224699100-224699101
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	GATA3	chr1:224698394-224699305	SK-N-SH	brain:	n/a	chr1:224699221-224699231
2	GATA3	chr1:224698583-224699269	MCF-7	breast:	n/a	chr1:224699221-224699231
3	FOXA2	chr1:224698959-224699178	HepG2	liver:	n/a	n/a
4	GATA3	chr1:224698701-224699359	MCF-7	breast:	n/a	chr1:224699221-224699231
5	FOXA1	chr1:224698845-224699303	HepG2	liver:	n/a	n/a
6	GATA3	chr1:224698411-224699276	SK-N-SH	brain:	n/a	chr1:224699221-224699231
7	SIN3AK20	chr1:224698535-224699295	MCF-7	breast:	n/a	n/a
8	TCF12	chr1:224698432-224699284	SK-N-SH	brain:	n/a	n/a
9	GATA2	chr1:224698543-224699139	SH-SY5Y	brain:	n/a	n/a
10	FOXA1	chr1:224698983-224699208	HepG2	liver:	n/a	n/a
11	GATA2	chr1:224698746-224699112	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:224693369..224695979-chr1:224697952..224700518,2	K562	blood:

Variant related genes	Relation type
CNIH3	TF binding region

Extended variants
information (count: 15 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs11578709	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11584057	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17570292	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs34119581	0.95[AFR][1000 genomes]
rs35804313	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs35915186	0.82[AMR][1000 genomes]
rs6426134	0.85[AFR][1000 genomes]
rs66530931	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6682205	0.95[AFR][1000 genomes]
rs6698343	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs67267495	0.87[ASN][1000 genomes]
rs71644786	0.80[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv8868	chr1:224383023-224752531	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv1014717	chr1:224551939-224885543	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv535311	chr1:224551939-224885543	Strong transcription Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6678608	CNIH4	cis	Esophagus Muscularis	GTEx
rs6678608	CNIH4	cis	Thyroid	GTEx
rs6678608	CNIH4	cis	Muscle Skeletal	GTEx

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:224690000-224699400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr1:224690000-224702000	Enhancers	Liver	Liver
3	chr1:224692000-224701600	Weak transcription	Fetal Lung	lung
4	chr1:224692400-224701600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr1:224692600-224700600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr1:224693600-224699200	Enhancers	Rectal Mucosa Donor 31	rectum
7	chr1:224694200-224704000	Weak transcription	Right Atrium	heart
8	chr1:224694200-224717600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr1:224694200-224727600	Weak transcription	Brain Anterior Caudate	brain
10	chr1:224696400-224701200	Weak transcription	Fetal Kidney	kidney
11	chr1:224696400-224716600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr1:224697000-224699200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr1:224697000-224699400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr1:224697000-224699400	Enhancers	Rectal Mucosa Donor 29	rectum
15	chr1:224697000-224700000	Enhancers	Breast Myoepithelial Primary Cells	Breast
16	chr1:224697200-224699200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr1:224697200-224699200	Enhancers	Fetal Intestine Small	intestine
18	chr1:224697200-224699200	Enhancers	K562	blood
19	chr1:224697200-224699200	Enhancers	NHEK	skin
20	chr1:224697200-224699400	Enhancers	Fetal Thymus	thymus
21	chr1:224697200-224699400	Enhancers	NHLF	lung
22	chr1:224697200-224699600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr1:224697200-224702200	Enhancers	Dnd41	blood
24	chr1:224697400-224699200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr1:224697400-224699200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr1:224697600-224699200	Enhancers	NH-A	brain
27	chr1:224697800-224699200	Enhancers	Osteobl	bone
28	chr1:224698200-224700600	Weak transcription	Duodenum Mucosa	Duodenum
29	chr1:224698400-224699200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr1:224698400-224699200	Enhancers	HSMM	muscle
31	chr1:224698400-224699200	Enhancers	HSMMtube	muscle
32	chr1:224698400-224699400	Enhancers	Thymus	Thymus
33	chr1:224698400-224699400	Enhancers	HMEC	breast
34	chr1:224698600-224700600	Weak transcription	Fetal Intestine Large	intestine
35	chr1:224698600-224701200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr1:224698600-224701200	Weak transcription	Adipose Nuclei	Adipose
37	chr1:224698600-224701400	Weak transcription	Ovary	ovary
38	chr1:224698600-224701400	Weak transcription	Skeletal Muscle Female	skeletal muscle
39	chr1:224698800-224699200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr1:224698800-224699200	Enhancers	Stomach Smooth Muscle	stomach
41	chr1:224698800-224700000	Weak transcription	HepG2	liver
42	chr1:224698800-224701000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr1:224698800-224701200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
44	chr1:224698800-224701200	Weak transcription	Duodenum Smooth Muscle	Duodenum
45	chr1:224698800-224701400	Weak transcription	HUES6 Cell Line	embryonic stem cell
46	chr1:224699000-224699400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr1:224699000-224700200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
48	chr1:224699000-224700400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr1:224699000-224700600	Weak transcription	Stomach Mucosa	stomach
50	chr1:224699000-224701400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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