Variant report

Variant	rs2233427
Chromosome Location	chr6:44233704-44233705
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	CBX3	chr6:44232458-44233942	K562	blood:	n/a	n/a
2	HCFC1	chr6:44232499-44233787	Hela-S3	cervix:	n/a	n/a
3	CTCF	chr6:44232434-44233888	SK-N-SH	brain:	n/a	n/a
4	MTA3	chr6:44229597-44234687	GM12878	blood:	n/a	n/a
5	RELA	chr6:44229670-44234939	GM12891	blood:	n/a	chr6:44230761-44230770 chr6:44230761-44230770 chr6:44231328-44231337 chr6:44231328-44231337
6	MAZ	chr6:44230296-44234445	IMR90	lung:	n/a	n/a
7	ELF1	chr6:44232862-44233770	MCF-7	breast:	n/a	n/a
8	ESRRA	chr6:44222591-44234485	GM12878	blood:	n/a	chr6:44225492-44225508 chr6:44225493-44225512 chr6:44225493-44225507 chr6:44225491-44225509 chr6:44231630-44231646 chr6:44225492-44225502
9	NFIC	chr6:44233264-44233754	GM12878	blood:	n/a	n/a
10	MXI1	chr6:44232308-44233793	SK-N-SH	brain:	n/a	n/a
11	JUN	chr6:44231131-44234426	K562	blood:	n/a	n/a
12	CHD1	chr6:44232192-44233721	IMR90	lung:	n/a	n/a
13	NR2F2	chr6:44233002-44233760	K562	blood:	n/a	n/a
14	RUNX3	chr6:44231904-44233748	GM12878	blood:	n/a	n/a
15	POLR2A	chr6:44232957-44233801	SK-N-MC	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:44229152..44231602-chr6:44233591..44236343,2	MCF-7	breast:
2	chr6:44231911..44234847-chr6:44237510..44240187,2	MCF-7	breast:
3	chr6:44233082..44237547-chr6:44353791..44357282,5	MCF-7	breast:
4	chr6:44092343..44095710-chr6:44231665..44234902,4	K562	blood:
5	chr6:44231291..44234957-chr6:44353668..44356659,3	K562	blood:
6	chr6:44233695..44236268-chr6:44306586..44308563,3	K562	blood:
7	chr6:44231156..44234544-chr6:44279395..44281173,3	MCF-7	breast:
8	chr6:44231603..44235224-chr6:44277267..44282023,5	MCF-7	breast:

Variant related genes	Relation type
TMEM151B	TF binding region
NFKBIE	TF binding region
ENSG00000180992	Chromatin interaction
ENSG00000137216	Chromatin interaction
ENSG00000096401	Chromatin interaction
ENSG00000124608	Chromatin interaction
ENSG00000178233	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs2233424	0.81[AFR][1000 genomes]
rs2233431	0.96[AFR][1000 genomes]
rs2233434	1.00[AFR][1000 genomes]
rs28362854	1.00[AFR][1000 genomes]
rs28362856	1.00[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931987	chr6:43624625-44350167	Enhancers Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	201 gene(s)	inside rSNPs	diseases
2	nsv885851	chr6:44178471-44240559	Strong transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	100 gene(s)	inside rSNPs	diseases
3	nsv603003	chr6:44191920-44253765	Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
4	nsv462936	chr6:44191920-44282316	Weak transcription Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
5	nsv603004	chr6:44191920-44282316	Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
6	nsv885853	chr6:44197181-44274797	Weak transcription Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
7	nsv524398	chr6:44200953-44253765	Active TSS Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
8	nsv885854	chr6:44211867-44274797	Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
9	nsv462937	chr6:44211867-44279111	Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
10	nsv603005	chr6:44211867-44279111	Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
11	nsv885857	chr6:44223010-44250165	Flanking Active TSS Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	28 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:44231400-44233800	Active TSS	Pancreatic Islets	Pancreatic Islet
2	chr6:44231800-44233800	Active TSS	Primary T helper cells PMA-I stimulated	--
3	chr6:44232600-44233800	Active TSS	Primary T killer memory cells from peripheral blood	blood
4	chr6:44232800-44233800	Active TSS	Thymus	Thymus
5	chr6:44232800-44234200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr6:44233000-44233800	Active TSS	Rectal Mucosa Donor 29	rectum
7	chr6:44233000-44233800	Active TSS	Skeletal Muscle Female	skeletal muscle
8	chr6:44233000-44236000	Weak transcription	Fetal Heart	heart
9	chr6:44233200-44233800	Active TSS	Stomach Smooth Muscle	stomach
10	chr6:44233200-44234000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr6:44233400-44233800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr6:44233400-44233800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr6:44233400-44233800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
14	chr6:44233400-44233800	Enhancers	Adipose Nuclei	Adipose
15	chr6:44233400-44233800	Weak transcription	Spleen	Spleen
16	chr6:44233400-44234000	Flanking Active TSS	Primary B cells from peripheral blood	blood
17	chr6:44233400-44234000	Enhancers	Primary T helper naive cells from peripheral blood	blood
18	chr6:44233400-44234000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr6:44233400-44235800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr6:44233400-44235800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr6:44233400-44235800	Weak transcription	Brain Hippocampus Middle	brain
22	chr6:44233400-44236000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr6:44233400-44236000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr6:44233400-44236200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr6:44233400-44236200	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr6:44233400-44237000	Weak transcription	HMEC	breast
27	chr6:44233400-44237200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr6:44233400-44237400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
29	chr6:44233400-44237800	Weak transcription	Pancreas	Pancrea
30	chr6:44233400-44237800	Weak transcription	Right Ventricle	heart
31	chr6:44233600-44233800	Enhancers	H1 Cell Line	embryonic stem cell
32	chr6:44233600-44233800	Enhancers	HUES6 Cell Line	embryonic stem cell
33	chr6:44233600-44233800	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
34	chr6:44233600-44233800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
35	chr6:44233600-44233800	Enhancers	Primary B cells from cord blood	blood
36	chr6:44233600-44233800	Flanking Active TSS	Primary T cells from cord blood	blood
37	chr6:44233600-44233800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
38	chr6:44233600-44233800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
39	chr6:44233600-44233800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
40	chr6:44233600-44233800	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr6:44233600-44233800	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
42	chr6:44233600-44233800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr6:44233600-44233800	Enhancers	Cortex derived primary cultured neurospheres	brain
44	chr6:44233600-44233800	Enhancers	Brain Germinal Matrix	brain
45	chr6:44233600-44233800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
46	chr6:44233600-44233800	Enhancers	Fetal Intestine Large	intestine
47	chr6:44233600-44233800	Enhancers	Fetal Muscle Trunk	muscle
48	chr6:44233600-44233800	Enhancers	Fetal Stomach	stomach
49	chr6:44233600-44233800	Enhancers	Dnd41	blood
50	chr6:44233600-44233800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links