Variant report

Variant	rs240374
Chromosome Location	chr6:75994151-75994152
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	REST	chr6:75993833-75995120	H1-neurons	neurons:	n/a	n/a
2	POLR2A	chr6:75994084-75995371	GM15510	blood:	n/a	n/a
3	TCF12	chr6:75993986-75995043	ECC-1	luminal epithelium:	n/a	n/a
4	MAZ	chr6:75994090-75995082	Hela-S3	cervix:	n/a	n/a
5	IRF1	chr6:75994058-75995666	K562	blood:	n/a	chr6:75994537-75994551 chr6:75995171-75995181 chr6:75995651-75995665 chr6:75995651-75995661 chr6:75994538-75994555
6	GABPA	chr6:75994014-75995067	MCF-7	breast:	n/a	chr6:75994713-75994722 chr6:75994713-75994724 chr6:75994710-75994724 chr6:75994713-75994727
7	MAX	chr6:75993992-75995227	K562	blood:	n/a	n/a
8	ZNF263	chr6:75993583-75995340	HEK293-T-REx	kidney:	n/a	chr6:75994071-75994080 chr6:75994607-75994628 chr6:75994582-75994603
9	CHD2	chr6:75993943-75995329	K562	blood:	n/a	n/a
10	ZBTB7A	chr6:75993922-75994196	HepG2	liver:	n/a	n/a
11	POLR2A	chr6:75993826-75995472	GM19193	blood:	n/a	n/a
12	KAP1	chr6:75993808-75995377	HEK293	kidney:	n/a	n/a
13	EP300	chr6:75993616-75995335	GM12878	blood:	n/a	chr6:75995145-75995159 chr6:75993959-75993973
14	POLR2A	chr6:75994136-75995072	PANC-1	pancreas:	n/a	n/a
15	POLR2A	chr6:75994126-75995104	U87	brain:	n/a	n/a
16	RCOR1	chr6:75993947-75994910	HepG2	liver:	n/a	n/a
17	POLR2A	chr6:75993738-75995279	GM12878	blood:	n/a	n/a
18	TBP	chr6:75994050-75995106	K562	blood:	n/a	n/a
19	TBL1XR1	chr6:75993967-75994937	K562	blood:	n/a	n/a
20	POLR2A	chr6:75993696-75995461	HUVEC	blood vessel:	n/a	n/a
21	GABPA	chr6:75993984-75995640	HL-60	blood:	n/a	chr6:75994713-75994722 chr6:75994713-75994724 chr6:75994710-75994724 chr6:75994713-75994727
22	POLR2A	chr6:75993513-75995679	Hela-S3	cervix:	n/a	n/a
23	TCF12	chr6:75994002-75995197	A549	lung:	n/a	n/a
24	GABPA	chr6:75993913-75995245	A549	lung:	n/a	chr6:75994713-75994722 chr6:75994713-75994724 chr6:75994710-75994724 chr6:75994713-75994727
25	POLR2A	chr6:75993887-75995086	MCF-7	breast:	n/a	n/a
26	TAF1	chr6:75993776-75995079	H1-neurons	neurons:	n/a	n/a
27	SP1	chr6:75994041-75995122	HCT-116	colon:	n/a	chr6:75994501-75994515 chr6:75994619-75994630
28	GABPA	chr6:75993982-75994990	SK-N-SH	brain:	n/a	chr6:75994713-75994722 chr6:75994713-75994724 chr6:75994710-75994724 chr6:75994713-75994727
29	STAT1	chr6:75993707-75995140	GM12878	blood:	n/a	chr6:75994541-75994552
30	POLR2A	chr6:75993912-75995027	HUVEC	blood vessel:	n/a	n/a
31	STAT5A	chr6:75993554-75995351	GM12878	blood:	n/a	chr6:75994541-75994552
32	RELA	chr6:75993985-75995279	GM15510	blood:	n/a	n/a
33	POLR2A	chr6:75994113-75995166	GM12878	blood:	n/a	n/a
34	MAX	chr6:75994007-75995293	HCT-116	colon:	n/a	n/a
35	POLR2A	chr6:75993985-75995200	K562	blood:	n/a	n/a
36	MAX	chr6:75993958-75995133	MCF-7	breast:	n/a	n/a
37	GTF2F1	chr6:75994113-75995029	Hela-S3	cervix:	n/a	n/a
38	SIN3AK20	chr6:75994056-75995036	PANC-1	pancreas:	n/a	n/a
39	BHLHE40	chr6:75993846-75995819	K562	blood:	n/a	chr6:75995133-75995154
40	ZBTB7A	chr6:75993666-75994603	ECC-1	luminal epithelium:	n/a	n/a
41	ZNF143	chr6:75994020-75995269	GM12878	blood:	n/a	chr6:75995146-75995155
42	POLR2A	chr6:75994008-75995051	A549	lung:	n/a	n/a
43	MAZ	chr6:75993792-75995279	K562	blood:	n/a	n/a
44	POLR2A	chr6:75993671-75995124	H1-neurons	neurons:	n/a	n/a
45	POLR2A	chr6:75994089-75995071	MCF-7	breast:	n/a	n/a
46	POLR2A	chr6:75994084-75995132	HUVEC	blood vessel:	n/a	n/a
47	POLR2A	chr6:75993924-75995466	GM18951	blood:	n/a	n/a
48	MAX	chr6:75994125-75995131	ECC-1	luminal epithelium:	n/a	n/a
49	POLR2A	chr6:75993828-75995393	K562	blood:	n/a	n/a
50	POLR2A	chr6:75993742-75995036	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:75981554..75983680-chr6:75993870..75995991,2	K562	blood:
2	chr6:75951699..75955124-chr6:75992599..75996025,9	K562	blood:
3	chr6:75949911..75955499-chr6:75993041..75995715,6	MCF-7	breast:
4	chr6:75993142..75995708-chr6:76310246..76313188,4	K562	blood:
5	chr6:74180943..74183846-chr6:75992415..75994208,2	K562	blood:
6	chr6:75992636..75994360-chr6:75994591..75996094,2	K562	blood:
7	chr6:75982180..75984876-chr6:75993848..75995841,3	K562	blood:
8	chr6:75951366..75953542-chr6:75992434..75995845,4	K562	blood:
9	chr6:75951485..75954328-chr6:75992401..75995008,3	MCF-7	breast:
10	chr6:75993176..75995308-chr6:76310710..76312367,2	MCF-7	breast:
11	chr6:75959944..75962259-chr6:75992382..75994540,2	K562	blood:

Variant related genes	Relation type
ENSG00000225793	TF binding region
TMEM30A	TF binding region
ENSG00000135297	Chromatin interaction
ENSG00000112697	Chromatin interaction
ENSG00000225793	Chromatin interaction
ENSG00000112701	Chromatin interaction
ENSG00000112695	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs1018471	0.82[ASW][hapmap];0.89[LWK][hapmap];0.89[YRI][hapmap]
rs13191146	0.83[EUR][1000 genomes]
rs13193201	0.87[CEU][hapmap];0.92[TSI][hapmap];0.81[EUR][1000 genomes]
rs13198000	0.87[CEU][hapmap];0.92[TSI][hapmap];0.86[EUR][1000 genomes]
rs13201278	0.84[TSI][hapmap]
rs13211657	0.83[EUR][1000 genomes]
rs13211961	0.92[TSI][hapmap]
rs13213719	1.00[CEU][hapmap];0.92[TSI][hapmap];0.93[EUR][1000 genomes]
rs13214997	0.87[CEU][hapmap];0.92[TSI][hapmap]
rs13217015	0.87[CEU][hapmap];0.86[EUR][1000 genomes]
rs13217241	0.87[CEU][hapmap];0.83[EUR][1000 genomes]
rs13217398	0.87[CEU][hapmap];0.86[EUR][1000 genomes]
rs16886390	0.84[JPT][hapmap]
rs16886391	0.84[JPT][hapmap]
rs16886411	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2250989	0.83[ASW][hapmap];0.83[LWK][hapmap];1.00[YRI][hapmap]
rs240378	0.84[AFR][1000 genomes]
rs240379	1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs240388	0.92[JPT][hapmap]
rs240390	0.92[JPT][hapmap]
rs240423	0.84[JPT][hapmap]
rs240432	0.92[JPT][hapmap]
rs2703710	0.82[JPT][hapmap]
rs2748252	0.83[ASW][hapmap];0.93[LWK][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs2808191	0.82[JPT][hapmap]
rs2808196	0.82[JPT][hapmap]
rs2842457	0.82[JPT][hapmap]
rs2842459	1.00[YRI][hapmap]
rs2842462	0.83[ASW][hapmap];0.87[LWK][hapmap];1.00[YRI][hapmap]
rs2842463	0.83[ASW][hapmap];0.89[LWK][hapmap];1.00[YRI][hapmap]
rs2951933	0.82[JPT][hapmap]
rs2951935	0.81[JPT][hapmap]
rs2951948	0.81[JPT][hapmap]
rs2951953	0.82[JPT][hapmap]
rs2998376	0.82[JPT][hapmap]
rs3756794	0.91[ASN][1000 genomes]
rs3777512	0.97[ASN][1000 genomes]
rs3822870	0.90[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs414624	1.00[JPT][hapmap]
rs6453821	0.93[EUR][1000 genomes]
rs7741596	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1016804	chr6:75775846-76188585	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv538310	chr6:75775846-76188585	Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
3	nsv1024079	chr6:75848556-76238519	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
4	nsv1027915	chr6:75893542-76510113	Active TSS Enhancers Strong transcription Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
5	nsv538311	chr6:75893542-76510113	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
6	nsv603763	chr6:75923605-76009426	Genic enhancers Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
7	nsv603764	chr6:75963751-76025603	Weak transcription Active TSS Genic enhancers Enhancers Strong transcription ZNF genes & repeats Flanking 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	14 gene(s)	inside rSNPs	diseases
8	nsv830698	chr6:75968810-76115592	Strong transcription Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 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	chr6:75987800-75996200	Active TSS	GM12878-XiMat	blood
2	chr6:75989200-75995800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr6:75990000-75995400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr6:75990200-75996400	Active TSS	ES-I3 Cell Line	embryonic stem cell
5	chr6:75991000-75996000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr6:75991000-75996000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr6:75991200-75995400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr6:75991200-75995400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr6:75991400-75995200	Active TSS	iPS-20b Cell Line	embryonic stem cell
10	chr6:75991400-75995600	Active TSS	H1 Cell Line	embryonic stem cell
11	chr6:75991400-75995600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr6:75991400-75995600	Active TSS	HMEC	breast
13	chr6:75991400-75995600	Active TSS	NHLF	lung
14	chr6:75991600-75996000	Active TSS	Pancreatic Islets	Pancreatic Islet
15	chr6:75991600-75997000	Active TSS	A549	lung
16	chr6:75991800-75994200	Active TSS	Right Atrium	heart
17	chr6:75991800-75995400	Active TSS	Aorta	Aorta
18	chr6:75991800-75995600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
19	chr6:75991800-75995600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr6:75991800-75995800	Active TSS	NHDF-Ad	bronchial
21	chr6:75991800-75996400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr6:75991800-75997600	Active TSS	K562	blood
23	chr6:75992000-75995400	Active TSS	Rectal Mucosa Donor 29	rectum
24	chr6:75992000-75995600	Active TSS	NH-A	brain
25	chr6:75992000-75995800	Active TSS	iPS-15b Cell Line	embryonic stem cell
26	chr6:75992000-75995800	Active TSS	iPS-18 Cell Line	embryonic stem cell
27	chr6:75992000-75996400	Active TSS	HUES6 Cell Line	embryonic stem cell
28	chr6:75992200-75995400	Active TSS	HSMMtube	muscle
29	chr6:75992400-75995400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr6:75992400-75995400	Active TSS	Right Ventricle	heart
31	chr6:75992400-75995600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr6:75992400-75995600	Active TSS	Fetal Kidney	kidney
33	chr6:75992400-75995600	Active TSS	HSMM	muscle
34	chr6:75992600-75995200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr6:75992600-75995400	Active TSS	Colon Smooth Muscle	Colon
36	chr6:75992600-75995400	Active TSS	Ovary	ovary
37	chr6:75992600-75995600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
38	chr6:75992600-75995800	Active TSS	HUES64 Cell Line	embryonic stem cell
39	chr6:75992600-75995800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr6:75992800-75995200	Active TSS	Brain Hippocampus Middle	brain
41	chr6:75992800-75995200	Active TSS	Left Ventricle	heart
42	chr6:75992800-75995400	Active TSS	H9 Cell Line	embryonic stem cell
43	chr6:75992800-75995400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr6:75992800-75995400	Active TSS	Colonic Mucosa	Colon
45	chr6:75992800-75995400	Active TSS	Psoas Muscle	Psoas
46	chr6:75992800-75995600	Active TSS	Breast Myoepithelial Primary Cells	Breast
47	chr6:75992800-75995600	Active TSS	Brain Anterior Caudate	brain
48	chr6:75992800-75995600	Active TSS	Duodenum Mucosa	Duodenum
49	chr6:75992800-75995600	Active TSS	Duodenum Smooth Muscle	Duodenum
50	chr6:75992800-75995600	Active TSS	Fetal Intestine Small	intestine

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links