Variant report

Variant	rs3122711
Chromosome Location	chr1:212779914-212779915
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	POLR2A	chr1:212778466-212788906	MCF10A-Er-Src	breast:	n/a	n/a
2	TCF12	chr1:212779838-212780638	ECC-1	luminal epithelium:	n/a	n/a
3	POLR2A	chr1:212778349-212787926	MCF10A-Er-Src	breast:	n/a	n/a
4	ZBTB7A	chr1:212779716-212779930	K562	blood:	n/a	n/a
5	TCF12	chr1:212779886-212782525	A549	lung:	n/a	n/a
6	MYC	chr1:212779904-212780326	MCF10A-Er-Src	breast:	n/a	chr1:212780016-212780023 chr1:212780015-212780024
7	POLR2A	chr1:212779324-212788938	Hela-S3	cervix:	n/a	n/a
8	CHD1	chr1:212779286-212788865	IMR90	lung:	n/a	chr1:212783477-212783487 chr1:212782811-212782821
9	GATA2	chr1:212778641-212779919	HUVEC	blood vessel:	n/a	chr1:212778832-212778839 chr1:212778828-212778844 chr1:212779634-212779650 chr1:212779123-212779130 chr1:212778832-212778839 chr1:212779631-212779652 chr1:212779124-212779141 chr1:212779123-212779130 chr1:212779119-212779135 chr1:212779116-212779137 chr1:212779637-212779647 chr1:212779633-212779647 chr1:212779634-212779650 chr1:212779123-212779130 chr1:212779122-212779132 chr1:212778832-212778839
10	GATA3	chr1:212778488-212780448	T-47D	breast:	n/a	chr1:212778832-212778839 chr1:212780099-212780115 chr1:212778828-212778844 chr1:212779634-212779650 chr1:212779123-212779130 chr1:212778832-212778839 chr1:212779631-212779652 chr1:212779124-212779141 chr1:212779123-212779130 chr1:212779119-212779135 chr1:212779116-212779137 chr1:212779637-212779647 chr1:212780097-212780118 chr1:212779634-212779650 chr1:212779123-212779130 chr1:212779122-212779132 chr1:212778832-212778839
11	POLR2A	chr1:212779228-212783228	H1-neurons	neurons:	n/a	n/a
12	SUZ12	chr1:212779614-212781546	NT2-D1	testis:	n/a	n/a
13	GATA1	chr1:212778620-212780603	PBDE	blood:	n/a	chr1:212778832-212778839 chr1:212780099-212780115 chr1:212778828-212778844 chr1:212779634-212779650 chr1:212779123-212779130 chr1:212778832-212778839 chr1:212779631-212779652 chr1:212779124-212779141 chr1:212779123-212779130 chr1:212779119-212779135 chr1:212779116-212779137 chr1:212779637-212779647 chr1:212780097-212780118 chr1:212779634-212779650 chr1:212779123-212779130 chr1:212779122-212779132 chr1:212778832-212778839
14	MYC	chr1:212779907-212780491	MCF10A-Er-Src	breast:	n/a	chr1:212780016-212780023 chr1:212780015-212780024
15	HCFC1	chr1:212778936-212785331	Hela-S3	cervix:	n/a	n/a
16	GATA2	chr1:212779350-212780676	SH-SY5Y	brain:	n/a	chr1:212780099-212780115 chr1:212779634-212779650 chr1:212779631-212779652 chr1:212779637-212779647 chr1:212779633-212779647 chr1:212780097-212780118 chr1:212779634-212779650
17	GATA3	chr1:212779889-212780026	SH-SY5Y	brain:	n/a	n/a
18	JUN	chr1:212779768-212783900	K562	blood:	n/a	chr1:212782720-212782729 chr1:212781672-212781681 chr1:212783142-212783153 chr1:212781673-212781682 chr1:212782718-212782727 chr1:212780482-212780493 chr1:212781676-212781685 chr1:212781655-212781664 chr1:212782077-212782090 chr1:212782719-212782728 chr1:212782721-212782730 chr1:212782722-212782731
19	HA-E2F1	chr1:212779867-212780586	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:212730770..212733133-chr1:212778739..212783577,4	MCF-7	breast:
2	chr1:212588056..212590074-chr1:212779163..212783567,3	K562	blood:
3	chr1:212779176..212786217-chr1:213030148..213034937,8	K562	blood:
4	chr1:212777301..212780836-chr1:212781036..212784328,4	MCF-7	breast:
5	chr1:212729491..212744666-chr1:212778733..212791648,68	K562	blood:
6	chr1:212646206..212648127-chr1:212778382..212780130,2	K562	blood:
7	chr1:212752372..212753937-chr1:212778628..212781608,2	K562	blood:
8	chr1:212729172..212744062-chr1:212776412..212791648,77	K562	blood:
9	chr1:212779632..212786722-chr1:212965265..212968763,9	K562	blood:
10	chr1:212779632..212786722-chr1:212963640..212968604,10	K562	blood:

Variant related genes	Relation type
ATF3	TF binding region
ENSG00000260805	Chromatin interaction
ENSG00000203705	Chromatin interaction
ENSG00000162769	Chromatin interaction
ENSG00000198468	Chromatin interaction
ENSG00000117697	Chromatin interaction
ENSG00000162772	Chromatin interaction
ENSG00000065600	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs3122710	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3122713	0.90[ASN][1000 genomes]
rs3125297	0.90[ASN][1000 genomes]
rs9429889	0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv549139	chr1:212332294-212876902	Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
2	nsv1013110	chr1:212555764-212948092	Flanking Active TSS Bivalent/Poised TSS Strong transcription Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	81 gene(s)	inside rSNPs	diseases
3	nsv535287	chr1:212555764-212948092	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	81 gene(s)	inside rSNPs	diseases
4	esv2757770	chr1:212648143-212843103	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	77 gene(s)	inside rSNPs	diseases
5	esv2758996	chr1:212648143-212843103	Enhancers Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	77 gene(s)	inside rSNPs	diseases
6	nsv428588	chr1:212705588-212862875	Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	78 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212778000-212780200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr1:212778000-212780200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
3	chr1:212778200-212780000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr1:212778600-212780000	Bivalent Enhancer	Duodenum Mucosa	Duodenum
5	chr1:212778600-212780000	Enhancers	HMEC	breast
6	chr1:212778600-212780200	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr1:212778600-212780400	Bivalent Enhancer	HSMMtube	muscle
8	chr1:212778800-212780000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr1:212778800-212780000	Bivalent Enhancer	Primary T cells from cord blood	blood
10	chr1:212778800-212780200	Bivalent Enhancer	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr1:212778800-212780200	Bivalent Enhancer	Fetal Thymus	thymus
12	chr1:212778800-212780600	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr1:212778800-212780600	Bivalent Enhancer	Fetal Lung	lung
14	chr1:212779000-212780000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr1:212779000-212780000	Bivalent Enhancer	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr1:212779000-212780000	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr1:212779000-212780000	Enhancers	Colonic Mucosa	Colon
18	chr1:212779000-212780200	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr1:212779000-212780200	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
20	chr1:212779000-212780200	Bivalent Enhancer	Fetal Muscle Leg	muscle
21	chr1:212779000-212780800	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
22	chr1:212779200-212780000	Bivalent Enhancer	H9 Cell Line	embryonic stem cell
23	chr1:212779200-212780000	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
24	chr1:212779200-212780000	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
25	chr1:212779200-212780000	Bivalent Enhancer	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr1:212779200-212780000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr1:212779200-212780000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr1:212779200-212780000	Bivalent Enhancer	Left Ventricle	heart
29	chr1:212779200-212780000	Bivalent Enhancer	A549	lung
30	chr1:212779200-212780200	Bivalent Enhancer	Brain Dorsolateral Prefrontal Cortex	brain
31	chr1:212779200-212780400	Bivalent Enhancer	Colon Smooth Muscle	Colon
32	chr1:212779400-212780000	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
33	chr1:212779400-212780000	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr1:212779400-212780000	Enhancers	Brain Anterior Caudate	brain
35	chr1:212779400-212780000	Bivalent Enhancer	Brain Cingulate Gyrus	brain
36	chr1:212779400-212780000	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
37	chr1:212779400-212780000	Flanking Active TSS	Placenta	Placenta
38	chr1:212779400-212780000	Enhancers	Right Ventricle	heart
39	chr1:212779400-212780200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
40	chr1:212779400-212780200	Flanking Active TSS	NHEK	skin
41	chr1:212779400-212780400	Active TSS	Brain Substantia Nigra	brain
42	chr1:212779400-212781600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
43	chr1:212779400-212781800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr1:212779600-212780000	Bivalent Enhancer	Primary B cells from cord blood	blood
45	chr1:212779600-212780000	Bivalent Enhancer	Primary B cells from peripheral blood	blood
46	chr1:212779600-212780000	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
47	chr1:212779600-212780000	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 2	blood
48	chr1:212779600-212780000	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
49	chr1:212779600-212780000	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr1:212779600-212780000	Flanking Bivalent TSS/Enh	Stomach Mucosa	stomach

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