Variant report

Variant	rs1323322
Chromosome Location	chr6:56347700-56347701
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	FOXA1	chr6:56347257-56347783	HepG2	liver:	n/a	n/a
2	RCOR1	chr6:56347464-56347711	HepG2	liver:	n/a	n/a
3	HDAC2	chr6:56347328-56347727	HepG2	liver:	n/a	n/a
4	HNF4G	chr6:56347326-56347784	HepG2	liver:	n/a	chr6:56347565-56347580
5	MXI1	chr6:56347371-56347720	HepG2	liver:	n/a	n/a
6	RAD21	chr6:56347371-56347744	HepG2	liver:	n/a	n/a
7	HNF4G	chr6:56347310-56347756	HepG2	liver:	n/a	chr6:56347565-56347580
8	MAFK	chr6:56347439-56347800	HepG2	liver:	n/a	n/a
9	HNF4A	chr6:56347382-56347734	HepG2	liver:	n/a	chr6:56347564-56347579
10	RAD21	chr6:56347299-56347709	HepG2	liver:	n/a	n/a
11	ARID3A	chr6:56347324-56347724	HepG2	liver:	n/a	chr6:56347701-56347717
12	RAD21	chr6:56347361-56347703	HepG2	liver:	n/a	n/a
13	JUND	chr6:56347304-56347741	HepG2	liver:	n/a	n/a
14	SMC3	chr6:56347364-56347711	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:56347410..56349603-chr6:56406568..56408277,2	K562	blood:
2	chr6:56347192..56349659-chr6:56354834..56357164,3	K562	blood:
3	chr6:56347192..56349659-chr6:56354834..56357986,4	K562	blood:

Variant related genes	Relation type
DST	TF binding region
ENSG00000151914	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10456735	0.81[ASN][1000 genomes]
rs10484788	0.87[ASN][1000 genomes]
rs12196832	0.83[ASN][1000 genomes]
rs12663437	1.00[ASN][1000 genomes]
rs17757606	0.82[ASN][1000 genomes]
rs17830661	0.82[ASN][1000 genomes]
rs2281725	0.83[ASN][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	nsv491933	chr6:56177722-57171010	Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv830666	chr6:56243743-56419599	Genic enhancers Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv885912	chr6:56327849-56458836	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:56308800-56373800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr6:56315000-56349800	Strong transcription	HSMM	muscle
3	chr6:56315600-56371000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr6:56319000-56348200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr6:56319200-56348400	Strong transcription	NHDF-Ad	bronchial
6	chr6:56322200-56349200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr6:56322600-56348200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr6:56327200-56351400	Weak transcription	Fetal Thymus	thymus
9	chr6:56328600-56362000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr6:56329200-56373800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr6:56330000-56351400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
12	chr6:56330000-56372400	Weak transcription	Lung	lung
13	chr6:56330200-56357400	Weak transcription	Esophagus	oesophagus
14	chr6:56332800-56349200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr6:56333000-56350000	Strong transcription	HMEC	breast
16	chr6:56334400-56348200	Strong transcription	Fetal Muscle Trunk	muscle
17	chr6:56334400-56359400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr6:56337600-56348000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr6:56337600-56350800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr6:56337600-56351400	Weak transcription	Aorta	Aorta
21	chr6:56337600-56351400	Weak transcription	Pancreas	Pancrea
22	chr6:56337600-56364600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr6:56337600-56376000	Weak transcription	Gastric	stomach
24	chr6:56339800-56354400	Strong transcription	Skeletal Muscle Female	skeletal muscle
25	chr6:56339800-56355800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr6:56340200-56347800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr6:56341200-56348200	Strong transcription	NH-A	brain
28	chr6:56341400-56348200	Strong transcription	Osteobl	bone
29	chr6:56341400-56348600	Weak transcription	Hela-S3	cervix
30	chr6:56341600-56351400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr6:56341800-56407400	Weak transcription	Spleen	Spleen
32	chr6:56342400-56353200	Weak transcription	Primary hematopoietic stem cells	blood
33	chr6:56343200-56351400	Weak transcription	Brain Angular Gyrus	brain
34	chr6:56343600-56347800	Strong transcription	Muscle Satellite Cultured Cells	--
35	chr6:56343600-56349400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr6:56344200-56348200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr6:56344200-56348200	Strong transcription	Rectal Mucosa Donor 29	rectum
38	chr6:56344200-56371600	Strong transcription	HUES48 Cell Line	embryonic stem cell
39	chr6:56344400-56347800	Strong transcription	Brain Substantia Nigra	brain
40	chr6:56344400-56347800	Strong transcription	Monocytes-CD14+_RO01746	blood
41	chr6:56344400-56348000	Strong transcription	H1 Cell Line	embryonic stem cell
42	chr6:56344400-56348200	Strong transcription	Left Ventricle	heart
43	chr6:56344400-56348200	Strong transcription	HUVEC	blood vessel
44	chr6:56344400-56348400	Strong transcription	NHLF	lung
45	chr6:56344600-56347800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
46	chr6:56344600-56347800	Strong transcription	Stomach Smooth Muscle	stomach
47	chr6:56344600-56348200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr6:56344600-56348800	Strong transcription	HSMMtube	muscle
49	chr6:56344600-56351800	Weak transcription	A549	lung
50	chr6:56344600-56354200	Strong transcription	iPS-20b Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links