Variant report

Variant	rs2274972
Chromosome Location	chr6:71377711-71377712
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	POLR2A	chr6:71376772-71378355	GM12892	blood:	n/a	n/a
2	MXI1	chr6:71377057-71378418	Hela-S3	cervix:	n/a	n/a
3	ELF1	chr6:71377072-71377850	HCT-116	colon:	n/a	chr6:71377456-71377465 chr6:71377088-71377099 chr6:71377683-71377692 chr6:71377455-71377466 chr6:71377636-71377645
4	TAF1	chr6:71377086-71378032	ECC-1	luminal epithelium:	n/a	n/a
5	ELF1	chr6:71377236-71377817	SK-N-SH	brain:	n/a	chr6:71377456-71377465 chr6:71377683-71377692 chr6:71377455-71377466 chr6:71377636-71377645
6	MAX	chr6:71376971-71378309	ECC-1	luminal epithelium:	n/a	n/a
7	E2F4	chr6:71377269-71378419	K562	blood:	n/a	chr6:71377411-71377420 chr6:71377988-71377997 chr6:71377640-71377650 chr6:71378159-71378174
8	POLR2A	chr6:71377203-71378349	GM10847	blood:	n/a	n/a
9	POLR2A	chr6:71377169-71377790	HepG2	liver:	n/a	n/a
10	YY1	chr6:71377259-71377711	HCT-116	colon:	n/a	chr6:71377639-71377653 chr6:71377675-71377689 chr6:71377683-71377692 chr6:71377627-71377641
11	TBL1XR1	chr6:71377237-71377780	K562	blood:	n/a	n/a
12	RUNX3	chr6:71377105-71377877	GM12878	blood:	n/a	n/a
13	POLR2A	chr6:71377101-71377910	GM12878	blood:	n/a	n/a
14	GABPA	chr6:71377086-71377780	SK-N-SH	brain:	n/a	chr6:71377410-71377419 chr6:71377412-71377421 chr6:71377410-71377424 chr6:71377407-71377421 chr6:71377410-71377421
15	POLR2A	chr6:71377220-71378526	IMR90	lung:	n/a	n/a
16	SIN3AK20	chr6:71377281-71378302	PANC-1	pancreas:	n/a	n/a
17	POLR2A	chr6:71377185-71377887	HUVEC	blood vessel:	n/a	n/a
18	POLR2A	chr6:71377168-71378330	Hela-S3	cervix:	n/a	n/a
19	CHD2	chr6:71377134-71377793	K562	blood:	n/a	chr6:71377707-71377717
20	TAF1	chr6:71377203-71377718	SK-N-SH	brain:	n/a	n/a
21	CHD2	chr6:71377262-71377917	HepG2	liver:	n/a	chr6:71377707-71377717
22	POLR2A	chr6:71377129-71378340	GM18526	blood:	n/a	n/a
23	MXI1	chr6:71377009-71378379	HepG2	liver:	n/a	n/a
24	HEY1	chr6:71377202-71377997	HepG2	liver:	n/a	chr6:71377900-71377915 chr6:71377909-71377924 chr6:71377419-71377434 chr6:71377663-71377678
25	POLR2A	chr6:71376804-71377857	K562	blood:	n/a	n/a
26	TBP	chr6:71377126-71378396	H1-hESC	embryonic stem cell:	n/a	n/a
27	POLR2A	chr6:71377150-71377819	U87	brain:	n/a	n/a
28	PML	chr6:71377295-71377897	MCF-7	breast:	n/a	n/a
29	YY1	chr6:71377213-71377980	GM12878	blood:	n/a	chr6:71377639-71377653 chr6:71377675-71377689 chr6:71377683-71377692 chr6:71377902-71377913 chr6:71377627-71377641
30	ELK1	chr6:71377103-71377765	GM12878	blood:	n/a	n/a
31	YY1	chr6:71377176-71377914	GM12878	blood:	n/a	chr6:71377639-71377653 chr6:71377675-71377689 chr6:71377683-71377692 chr6:71377902-71377913 chr6:71377627-71377641
32	SP1	chr6:71377377-71377750	GM12878	blood:	n/a	chr6:71377489-71377498 chr6:71377707-71377719 chr6:71377488-71377502 chr6:71377532-71377546 chr6:71377708-71377717 chr6:71377482-71377496 chr6:71377709-71377718 chr6:71377481-71377493 chr6:71377483-71377492 chr6:71377708-71377717
33	YY1	chr6:71377105-71378331	H1-hESC	embryonic stem cell:	n/a	chr6:71377639-71377653 chr6:71377979-71377993 chr6:71377675-71377689 chr6:71377683-71377692 chr6:71377902-71377913 chr6:71377627-71377641 chr6:71378027-71378036
34	SMARCB1	chr6:71377119-71378432	Hela-S3	cervix:	n/a	n/a
35	TEAD4	chr6:71376967-71377798	K562	blood:	n/a	n/a
36	MAZ	chr6:71376982-71378452	IMR90	lung:	n/a	n/a
37	E2F6	chr6:71377064-71378275	K562	blood:	n/a	chr6:71377411-71377420 chr6:71377988-71377997 chr6:71377640-71377650 chr6:71378159-71378174
38	YY1	chr6:71377419-71377853	SK-N-SH_RA	brain:	n/a	chr6:71377639-71377653 chr6:71377675-71377689 chr6:71377683-71377692 chr6:71377627-71377641
39	POLR2A	chr6:71377156-71377868	U87	brain:	n/a	n/a
40	MTA3	chr6:71376710-71378399	GM12878	blood:	n/a	n/a
41	POLR2A	chr6:71377151-71378216	H1-hESC	embryonic stem cell:	n/a	n/a
42	POLR2A	chr6:71377264-71377840	HepG2	liver:	n/a	n/a
43	POLR2A	chr6:71376668-71378316	Raji	blood:	n/a	n/a
44	POLR2A	chr6:71377228-71377938	HepG2	liver:	n/a	n/a
45	POLR2A	chr6:71377184-71378302	A549	lung:	n/a	n/a
46	POLR2A	chr6:71377156-71377721	U87	brain:	n/a	n/a
47	RCOR1	chr6:71376778-71378307	K562	blood:	n/a	n/a
48	POLR2A	chr6:71377524-71377823	GM12891	blood:	n/a	n/a
49	CHD2	chr6:71377324-71378192	H1-hESC	embryonic stem cell:	n/a	chr6:71377707-71377717
50	SIN3AK20	chr6:71377392-71377810	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:139554231..139554819-chr6:71377322..71378009,2	Hela-S3	cervix:
2	chr17:56708748..56709679-chr6:71377382..71377916,2	Hela-S3	cervix:
3	chr6:71276528..71278152-chr6:71377519..71380132,3	MCF-7	breast:
4	chr6:71103256..71105709-chr6:71376472..71378763,2	K562	blood:
5	chr1:28832329..28832880-chr6:71377281..71377958,2	HCT-116	colon:
6	chr6:71275193..71277991-chr6:71376243..71378994,4	MCF-7	breast:

Variant related genes	Relation type
SLC25A6P6	TF binding region
ENSG00000154079	Chromatin interaction
ENSG00000180198	Chromatin interaction
ENSG00000120306	Chromatin interaction
ENSG00000212195	Chromatin interaction
ENSG00000237643	Chromatin interaction
ENSG00000242125	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs3734369	0.97[EUR][1000 genomes]
rs4706460	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4707842	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4707844	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61001507	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6902786	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6919104	0.80[AFR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6940971	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6941789	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7747310	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7748778	0.97[EUR][1000 genomes]
rs7754217	0.83[AFR][1000 genomes]
rs7764445	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9342796	1.00[EUR][1000 genomes]
rs9346403	0.92[EUR][1000 genomes]
rs9351793	0.85[AFR][1000 genomes]
rs9354937	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9354938	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9360426	0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9364102	0.84[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs9364103	0.85[AFR][1000 genomes]
rs9364109	0.92[EUR][1000 genomes]
rs9364111	0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932111	chr6:70736835-71633094	Enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv1027049	chr6:70961610-71561488	Strong transcription Active TSS Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv524328	chr6:70961833-71558805	Flanking Bivalent TSS/Enh Active TSS Weak transcription Strong transcription ZNF genes & repeats Enhancers Bivalent Enhancer Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	nsv917312	chr6:70961903-71601688	Enhancers Genic enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
5	nsv886147	chr6:71273253-71471863	Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:71376600-71378400	Active TSS	HUES64 Cell Line	embryonic stem cell
2	chr6:71376600-71378800	Active TSS	HSMMtube	muscle
3	chr6:71376600-71379400	Active TSS	Brain Inferior Temporal Lobe	brain
4	chr6:71376800-71378600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr6:71376800-71378800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
6	chr6:71376800-71378800	Active TSS	Fetal Muscle Trunk	muscle
7	chr6:71376800-71379000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr6:71376800-71379000	Active TSS	Rectal Smooth Muscle	rectum
9	chr6:71376800-71379200	Active TSS	ES-I3 Cell Line	embryonic stem cell
10	chr6:71376800-71379200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr6:71376800-71379200	Active TSS	A549	lung
12	chr6:71377000-71378200	Active TSS	Brain Cingulate Gyrus	brain
13	chr6:71377000-71378400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr6:71377000-71378400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
15	chr6:71377000-71378400	Active TSS	Brain Angular Gyrus	brain
16	chr6:71377000-71378400	Active TSS	Brain Hippocampus Middle	brain
17	chr6:71377000-71378400	Active TSS	Colon Smooth Muscle	Colon
18	chr6:71377000-71378600	Active TSS	Aorta	Aorta
19	chr6:71377000-71378600	Active TSS	Fetal Brain Male	brain
20	chr6:71377000-71378600	Active TSS	Left Ventricle	heart
21	chr6:71377000-71378600	Active TSS	Ovary	ovary
22	chr6:71377000-71378800	Active TSS	H9 Cell Line	embryonic stem cell
23	chr6:71377000-71378800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr6:71377000-71378800	Active TSS	Pancreatic Islets	Pancreatic Islet
25	chr6:71377000-71378800	Active TSS	HSMM	muscle
26	chr6:71377000-71379000	Active TSS	Breast Myoepithelial Primary Cells	Breast
27	chr6:71377000-71379000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
28	chr6:71377000-71379000	Active TSS	Fetal Muscle Leg	muscle
29	chr6:71377000-71379000	Active TSS	NHDF-Ad	bronchial
30	chr6:71377000-71379200	Active TSS	Psoas Muscle	Psoas
31	chr6:71377000-71379400	Active TSS	Colonic Mucosa	Colon
32	chr6:71377000-71379400	Active TSS	Right Atrium	heart
33	chr6:71377200-71377800	Active TSS	Fetal Brain Female	brain
34	chr6:71377200-71378000	Active TSS	Primary hematopoietic stem cells	blood
35	chr6:71377200-71378000	Active TSS	Primary T regulatory cells fromperipheralblood	blood
36	chr6:71377200-71378000	Active TSS	Stomach Smooth Muscle	stomach
37	chr6:71377200-71378200	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr6:71377200-71378200	Active TSS	Primary T cells from cord blood	blood
39	chr6:71377200-71378200	Active TSS	Primary T helper cells PMA-I stimulated	--
40	chr6:71377200-71378200	Active TSS	Primary T killer naive cells fromperipheralblood	blood
41	chr6:71377200-71378200	Active TSS	Primary T killer memory cells from peripheral blood	blood
42	chr6:71377200-71378200	Active TSS	Adipose Nuclei	Adipose
43	chr6:71377200-71378200	Active TSS	Liver	Liver
44	chr6:71377200-71378200	Active TSS	Brain Substantia Nigra	brain
45	chr6:71377200-71378200	Active TSS	Fetal Adrenal Gland	Adrenal Gland
46	chr6:71377200-71378200	Active TSS	Fetal Lung	lung
47	chr6:71377200-71378200	Active TSS	Fetal Stomach	stomach
48	chr6:71377200-71378200	Active TSS	Placenta Amnion	Placenta Amnion
49	chr6:71377200-71378200	Active TSS	Rectal Mucosa Donor 31	rectum
50	chr6:71377200-71378200	Active TSS	NHEK	skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links