Variant report

Variant	rs41269277
Chromosome Location	chr6:27835401-27835402
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:295)
CpG islands
(count:244)
Chromatin interactive
region (count:23)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:295 , 50 per page) page: 1 2 3 4 5 6

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ATF2	chr6:27834115-27835485	GM12878	blood:	n/a	n/a
2	MAX	chr6:27835063-27835564	SK-N-SH	brain:	n/a	n/a
3	POU2F2	chr6:27834251-27835517	GM12891	blood:	n/a	chr6:27834299-27834320
4	TCF12	chr6:27834676-27835477	GM12878	blood:	n/a	n/a
5	POLR2A	chr6:27831639-27835944	MCF-7	breast:	n/a	n/a
6	NFIC	chr6:27832621-27835576	GM12878	blood:	n/a	n/a
7	TAF7	chr6:27832651-27836396	H1-hESC	embryonic stem cell:	n/a	n/a
8	CEBPD	chr6:27833466-27835530	K562	blood:	n/a	n/a
9	TAF1	chr6:27833784-27835580	H1-hESC	embryonic stem cell:	n/a	n/a
10	YY1	chr6:27835111-27835466	SK-N-SH_RA	brain:	n/a	chr6:27835445-27835454
11	TBP	chr6:27835135-27835564	H1-hESC	embryonic stem cell:	n/a	n/a
12	POLR2A	chr6:27834965-27835439	A549	lung:	n/a	n/a
13	POLR2A	chr6:27831681-27835663	MCF-7	breast:	n/a	n/a
14	JUND	chr6:27833370-27835526	SK-N-SH	brain:	n/a	chr6:27834282-27834291
15	YY1	chr6:27834325-27835432	K562	blood:	n/a	chr6:27834547-27834559
16	STAT5A	chr6:27832583-27835747	GM12878	blood:	n/a	chr6:27835602-27835610
17	CREB1	chr6:27833361-27835634	GM12878	blood:	n/a	n/a
18	POLR2A	chr6:27832618-27835481	GM12891	blood:	n/a	n/a
19	ZEB1	chr6:27834448-27835590	HepG2	liver:	n/a	n/a
20	TEAD4	chr6:27834573-27835593	SK-N-SH	brain:	n/a	n/a
21	SIN3AK20	chr6:27835156-27835436	H1-hESC	embryonic stem cell:	n/a	n/a
22	ELF1	chr6:27833747-27835539	GM12878	blood:	n/a	n/a
23	YY1	chr6:27834077-27835531	GM12878	blood:	n/a	chr6:27834547-27834559 chr6:27835445-27835454
24	POLR2A	chr6:27832869-27835570	Gliobla	brain:	n/a	n/a
25	FOXM1	chr6:27832627-27835722	GM12878	blood:	n/a	n/a
26	POLR2A	chr6:27832745-27835566	GM10847	blood:	n/a	n/a
27	POLR2A	chr6:27832732-27835534	HUVEC	blood vessel:	n/a	n/a
28	TAF1	chr6:27835012-27835480	K562	blood:	n/a	n/a
29	TAF1	chr6:27835047-27835422	K562	blood:	n/a	n/a
30	PML	chr6:27832883-27835592	MCF-7	breast:	n/a	n/a
31	TAF1	chr6:27834966-27835619	MCF-7	breast:	n/a	n/a
32	POLR2A	chr6:27832669-27835567	MCF10A-Er-Src	breast:	n/a	n/a
33	RELA	chr6:27833925-27835514	GM18526	blood:	n/a	n/a
34	HEY1	chr6:27832629-27835529	K562	blood:	n/a	chr6:27832940-27832949 chr6:27832942-27832951
35	POLR2A	chr6:27832608-27835555	GM15510	blood:	n/a	n/a
36	MAX	chr6:27834292-27835469	H1-hESC	embryonic stem cell:	n/a	n/a
37	CTCF	chr6:27835240-27835530	HPF	lung:	n/a	n/a
38	MYC	chr6:27833855-27836057	NB4	blood:	n/a	n/a
39	ZKSCAN1	chr6:27834992-27835486	Hela-S3	cervix:	n/a	n/a
40	SP1	chr6:27835099-27835576	GM12878	blood:	n/a	chr6:27835402-27835423
41	ELF1	chr6:27834511-27835554	GM12878	blood:	n/a	n/a
42	POLR2A	chr6:27832654-27835691	SK-N-MC	brain:	n/a	n/a
43	POLR2A	chr6:27832719-27835560	GM12878	blood:	n/a	n/a
44	POLR2A	chr6:27834083-27835506	HepG2	liver:	n/a	n/a
45	POLR2A	chr6:27832846-27835535	PFSK-1	brain:	n/a	n/a
46	CTCF	chr6:27835360-27835510	HFF	foreskin:	n/a	n/a
47	PBX3	chr6:27835033-27835576	SK-N-SH	brain:	n/a	n/a
48	POLR2A	chr6:27835079-27835573	H1-neurons	neurons:	n/a	n/a
49	POLR2A	chr6:27832605-27835544	GM12878	blood:	n/a	n/a
50	BCL3	chr6:27834257-27835414	GM12878	blood:	n/a	n/a

(count:244 , 50 per page) page: 1 2 3 4 5

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr6:27835385-27835435	SK-N-MC	brain:	n/a
2	chr6:27835378-27835428	NH-A	brain:	n/a
3	chr6:27835363-27835413	HRCEpiC	kidney:	n/a
4	chr6:27835363-27835413	PrEC	prostate:	n/a
5	chr6:27835378-27835428	BJ	skin:	n/a
6	chr6:27835363-27835413	T-47D	breast:	n/a
7	chr6:27835378-27835428	HPAEpiC	pulmonary alveolar:	n/a
8	chr6:27835363-27835413	SK-N-MC	brain:	n/a
9	chr6:27835378-27835428	AG04450	lung:	fetal
10	chr6:27835400-27835450	ProgFib	skin:	n/a
11	chr6:27835378-27835428	AG09309	skin:	n/a
12	chr6:27835385-27835435	AG04450	lung:	fetal
13	chr6:27835378-27835428	HL-60	blood:	n/a
14	chr6:27835400-27835450	CMK	blood:	n/a
15	chr6:27835363-27835413	U87	brain:	n/a
16	chr6:27835363-27835413	Jurkat	blood:	n/a
17	chr6:27835400-27835450	T-47D	breast:	n/a
18	chr6:27835400-27835450	HEK293	kidney:	embryo
19	chr6:27835363-27835413	GM12878	blood:	n/a
20	chr6:27835400-27835450	AG04450	lung:	fetal
21	chr6:27835363-27835413	NB4	blood:	n/a
22	chr6:27835400-27835450	Jurkat	blood:	n/a
23	chr6:27835378-27835428	SK-N-SH	brain:	n/a
24	chr6:27835378-27835428	HIPEpiC	eye:	n/a
25	chr6:27835378-27835428	ECC-1	luminal epithelium:	n/a
26	chr6:27835385-27835435	ECC-1	luminal epithelium:	n/a
27	chr6:27835385-27835435	HRE	kidney:	n/a
28	chr6:27835363-27835413	MCF10A-Er-Src	breast:	n/a
29	chr6:27835363-27835413	AG09309	skin:	n/a
30	chr6:27835385-27835435	PrEC	prostate:	n/a
31	chr6:27835378-27835428	LNCaP	prostate:	n/a
32	chr6:27835378-27835428	Hepatocyte	liver:	n/a
33	chr6:27835363-27835413	RPTEC	kidney:	n/a
34	chr6:27835363-27835413	Hela-S3	cervix:	n/a
35	chr6:27835385-27835435	AG04449	skin:	fetal
36	chr6:27835400-27835450	AoSMC	blood vessel:	n/a
37	chr6:27835400-27835450	K562	blood:	n/a
38	chr6:27835378-27835428	HCM	heart:	n/a
39	chr6:27835363-27835413	SAEC	small airway:	n/a
40	chr6:27835378-27835428	Hela-S3	cervix:	n/a
41	chr6:27835385-27835435	BJ	skin:	n/a
42	chr6:27835363-27835413	PFSK-1	brain:	n/a
43	chr6:27835363-27835413	A549	lung:	n/a
44	chr6:27835363-27835413	HL-60	blood:	n/a
45	chr6:27835400-27835450	HIPEpiC	eye:	n/a
46	chr6:27835363-27835413	HCT-116	colon:	n/a
47	chr6:27835378-27835428	MCF10A-Er-Src	breast:	n/a
48	chr6:27835385-27835435	HUVEC	blood vessel:	n/a
49	chr6:27835400-27835450	PFSK-1	brain:	n/a
50	chr6:27835378-27835428	NHBE	bronchial:	n/a

(count:23 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:26054611..26058222-chr6:27833185..27835454,4	MCF-7	breast:
2	chr1:116915588..116917427-chr6:27834235..27836471,2	MCF-7	breast:
3	chr6:26270106..26271660-chr6:27833787..27835479,2	MCF-7	breast:
4	chr1:11967132..11968839-chr6:27832941..27835901,2	MCF-7	breast:
5	chr6:26154866..26157028-chr6:27832028..27836151,3	MCF-7	breast:
6	chr6:26249129..26252003-chr6:27832611..27836378,6	MCF-7	breast:
7	chr17:56735249..56737009-chr6:27834194..27835800,2	MCF-7	breast:
8	chr6:26156108..26158898-chr6:27832756..27836611,3	MCF-7	breast:
9	chr6:27113081..27116777-chr6:27832860..27836046,4	K562	blood:
10	chr6:26033297..26035200-chr6:27833856..27836117,3	MCF-7	breast:
11	chr6:27105570..27109142-chr6:27832678..27836176,3	K562	blood:
12	chr6:27098287..27101143-chr6:27833943..27835585,2	MCF-7	breast:
13	chr6:27834624..27836124-chr7:99722099..99724739,2	MCF-7	breast:
14	chr6:26044265..26046503-chr6:27834017..27836277,2	MCF-7	breast:
15	chr6:26019660..26022685-chr6:27833901..27836758,3	MCF-7	breast:
16	chr6:27833103..27835859-chr6:28582647..28584529,2	K562	blood:
17	chr6:26123459..26125455-chr6:27834569..27837416,2	MCF-7	breast:
18	chr6:27113591..27118417-chr6:27832860..27835856,7	K562	blood:
19	chr1:149855909..149858308-chr6:27833822..27835971,2	MCF-7	breast:
20	chr6:26123458..26125812-chr6:27833699..27835902,2	K562	blood:
21	chr16:4663445..4665916-chr6:27834145..27836986,3	MCF-7	breast:
22	chr1:16840036..16842043-chr6:27834742..27837032,2	MCF-7	breast:
23	chr6:27113113..27117592-chr6:27831181..27837403,7	MCF-7	breast:

No data

Variant related genes	Relation type
HIST1H2BPS2	TF binding region
HIST1H1B	TF binding region
HIST1H2BPS2	CpG island
HIST1H1B	CpG island
ENSG00000137259	Chromatin interaction
ENSG00000168298	Chromatin interaction
ENSG00000256316	Chromatin interaction
ENSG00000180596	Chromatin interaction
ENSG00000153443	Chromatin interaction
ENSG00000197903	Chromatin interaction
ENSG00000124635	Chromatin interaction
ENSG00000187837	Chromatin interaction
ENSG00000214309	Chromatin interaction
ENSG00000198339	Chromatin interaction
ENSG00000158373	Chromatin interaction
ENSG00000261135	Chromatin interaction
ENSG00000196787	Chromatin interaction
ENSG00000180573	Chromatin interaction
ENSG00000163399	Chromatin interaction
ENSG00000184825	Chromatin interaction
ENSG00000197459	Chromatin interaction
ENSG00000206652	Chromatin interaction
ENSG00000184678	Chromatin interaction
ENSG00000256018	Chromatin interaction
ENSG00000232040	Chromatin interaction
ENSG00000202077	Chromatin interaction
ENSG00000199347	Chromatin interaction
ENSG00000196532	Chromatin interaction
ENSG00000198366	Chromatin interaction
ENSG00000265565	Chromatin interaction
ENSG00000196176	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs12181629	0.90[ASN][1000 genomes]
rs2021835	1.00[ASN][1000 genomes]
rs9461418	1.00[ASN][1000 genomes]
rs9468236	1.00[ASN][1000 genomes]
rs9468242	1.00[ASN][1000 genomes]
rs9468243	1.00[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	nsv1022797	chr6:27396961-27864277	Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	390 gene(s)	inside rSNPs	diseases
2	nsv432858	chr6:27719375-28011652	Flanking Active TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	387 gene(s)	inside rSNPs	diseases
3	nsv1017440	chr6:27734824-27864277	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	370 gene(s)	inside rSNPs	diseases
4	nsv1022173	chr6:27734824-27959408	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	379 gene(s)	inside rSNPs	diseases
5	nsv883512	chr6:27748631-27969004	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	379 gene(s)	inside rSNPs	diseases
6	nsv601208	chr6:27810626-27969004	Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	237 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:27830800-27835800	Active TSS	K562	blood
2	chr6:27831200-27835800	Active TSS	ES-I3 Cell Line	embryonic stem cell
3	chr6:27831200-27835800	Active TSS	H9 Cell Line	embryonic stem cell
4	chr6:27831400-27835600	Active TSS	HUES6 Cell Line	embryonic stem cell
5	chr6:27831600-27835600	Active TSS	iPS-20b Cell Line	embryonic stem cell
6	chr6:27831600-27835800	Active TSS	Fetal Kidney	kidney
7	chr6:27831800-27835600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
8	chr6:27831800-27835600	Active TSS	HUES64 Cell Line	embryonic stem cell
9	chr6:27831800-27835800	Active TSS	Aorta	Aorta
10	chr6:27832000-27835600	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
11	chr6:27832200-27835600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr6:27832200-27835600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr6:27832200-27836000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr6:27832600-27835600	Active TSS	iPS-15b Cell Line	embryonic stem cell
15	chr6:27832600-27835600	Active TSS	Dnd41	blood
16	chr6:27832800-27835600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr6:27832800-27835800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr6:27832800-27835800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr6:27833000-27835600	Flanking Active TSS	Adipose Nuclei	Adipose
20	chr6:27833000-27835600	Active TSS	Hela-S3	cervix
21	chr6:27833000-27835800	Active TSS	H1 Cell Line	embryonic stem cell
22	chr6:27833000-27835800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
23	chr6:27833200-27835600	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
24	chr6:27833200-27835600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
25	chr6:27833200-27835600	Flanking Active TSS	Primary B cells from peripheral blood	blood
26	chr6:27833200-27835600	Flanking Active TSS	Primary T cells fromperipheralblood	blood
27	chr6:27833200-27835600	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
28	chr6:27833200-27835800	Flanking Active TSS	Primary B cells from cord blood	blood
29	chr6:27833200-27836000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr6:27833200-27836200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr6:27833400-27835600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
32	chr6:27833400-27835600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
33	chr6:27833400-27835600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
34	chr6:27833400-27835600	Flanking Bivalent TSS/Enh	Brain Hippocampus Middle	brain
35	chr6:27833400-27835600	Enhancers	Spleen	Spleen
36	chr6:27833400-27836000	Flanking Active TSS	Primary T cells from cord blood	blood
37	chr6:27833400-27836000	Flanking Active TSS	Primary hematopoietic stem cells	blood
38	chr6:27833400-27836000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr6:27833800-27835600	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr6:27833800-27835800	Flanking Active TSS	HMEC	breast
41	chr6:27834000-27836000	Flanking Active TSS	NHEK	skin
42	chr6:27834200-27835800	Active TSS	Placenta Amnion	Placenta Amnion
43	chr6:27834400-27835600	Flanking Active TSS	Stomach Mucosa	stomach
44	chr6:27834400-27835800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
45	chr6:27834600-27835800	Active TSS	Thymus	Thymus
46	chr6:27834800-27835600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr6:27834800-27835600	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
48	chr6:27834800-27835600	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
49	chr6:27834800-27835600	Active TSS	HSMM	muscle
50	chr6:27834800-27835600	Active TSS	HSMMtube	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links