Variant report

Variant	rs201005
Chromosome Location	chr6:27804160-27804161
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:41)
CpG islands
(count:0)
Chromatin interactive
region (count:23)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:41 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CHD1	chr6:27804111-27807828	GM12878	blood:	n/a	chr6:27805473-27805483
2	BCLAF1	chr6:27802551-27808286	K562	blood:	n/a	chr6:27803234-27803242
3	MXI1	chr6:27804102-27804229	GM12878	blood:	n/a	n/a
4	POLR2A	chr6:27803974-27807891	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr6:27804083-27807980	MCF10A-Er-Src	breast:	n/a	n/a
6	HEY1	chr6:27804138-27807845	HepG2	liver:	n/a	n/a
7	POLR2A	chr6:27804066-27804354	SK-N-SH	brain:	n/a	n/a
8	POLR2A	chr6:27796592-27807059	K562	blood:	n/a	n/a
9	BCLAF1	chr6:27804008-27806702	K562	blood:	n/a	n/a
10	POLR2A	chr6:27803885-27807892	H1-hESC	embryonic stem cell:	n/a	n/a
11	PML	chr6:27803632-27808099	K562	blood:	n/a	n/a
12	POLR2A	chr6:27803841-27808080	HepG2	liver:	n/a	n/a
13	ARID3A	chr6:27803666-27804378	K562	blood:	n/a	n/a
14	POLR2A	chr6:27803911-27807364	K562	blood:	n/a	n/a
15	POLR2A	chr6:27804109-27804391	SK-N-SH	brain:	n/a	n/a
16	FOXA2	chr6:27804008-27804974	HepG2	liver:	n/a	n/a
17	TBL1XR1	chr6:27804006-27806533	K562	blood:	n/a	n/a
18	HEY1	chr6:27803986-27807970	K562	blood:	n/a	n/a
19	POLR2A	chr6:27804142-27806938	H1-hESC	embryonic stem cell:	n/a	n/a
20	TEAD4	chr6:27803995-27807868	K562	blood:	n/a	n/a
21	POLR2A	chr6:27804030-27807960	IMR90	lung:	n/a	n/a
22	JUN	chr6:27803737-27808547	K562	blood:	n/a	chr6:27806307-27806315 chr6:27807869-27807883 chr6:27806241-27806250 chr6:27807727-27807735
23	POLR2A	chr6:27803870-27808082	H1-hESC	embryonic stem cell:	n/a	n/a
24	EP300	chr6:27804153-27805681	K562	blood:	n/a	n/a
25	POLR2A	chr6:27804058-27807910	K562	blood:	n/a	n/a
26	HEY1	chr6:27803827-27808553	K562	blood:	n/a	n/a
27	MXI1	chr6:27804111-27808202	IMR90	lung:	n/a	n/a
28	POLR2A	chr6:27804146-27807837	K562	blood:	n/a	n/a
29	POLR2A	chr6:27803623-27808498	H1-hESC	embryonic stem cell:	n/a	n/a
30	POLR2A	chr6:27803982-27807925	PBDE	blood:	n/a	n/a
31	MXI1	chr6:27803400-27808288	SK-N-SH	brain:	n/a	n/a
32	POLR2A	chr6:27804010-27808207	HepG2	liver:	n/a	n/a
33	TEAD4	chr6:27803800-27806597	K562	blood:	n/a	n/a
34	TAF7	chr6:27803882-27807923	H1-hESC	embryonic stem cell:	n/a	n/a
35	POLR2A	chr6:27803994-27806603	HL-60	blood:	n/a	n/a
36	REST	chr6:27803579-27806924	H1-neurons	neurons:	n/a	n/a
37	POLR2A	chr6:27799219-27808508	K562	blood:	n/a	n/a
38	TAL1	chr6:27804111-27806598	K562	blood:	n/a	chr6:27804481-27804499
39	CHD1	chr6:27804063-27808105	IMR90	lung:	n/a	chr6:27805473-27805483
40	POLR2A	chr6:27803736-27809014	K562	blood:	n/a	n/a
41	CEBPB	chr6:27804124-27806574	K562	blood:	n/a	chr6:27804613-27804624 chr6:27805598-27805611 chr6:27805598-27805609

No data

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

No.	Distal block	Cell Line	Cell type
1	chr6:26197676..26199688-chr6:27803867..27806296,2	MCF-7	breast:
2	chr6:26283488..26285487-chr6:27802901..27805712,2	MCF-7	breast:
3	chr6:26032417..26034288-chr6:27803614..27806340,2	K562	blood:
4	chr21:36282480..36284217-chr6:27803211..27804732,2	K562	blood:
5	chr6:27803895..27805819-chr6:28090155..28092205,2	MCF-7	breast:
6	chr6:27098188..27105257-chr6:27800590..27808222,20	K562	blood:
7	chr6:26020717..26022368-chr6:27803376..27805048,2	MCF-7	breast:
8	chr6:27093465..27120217-chr6:27768366..27817187,256	K562	blood:
9	chr3:6645512..6648049-chr6:27803536..27805535,2	K562	blood:
10	chr6:26201657..26204430-chr6:27803737..27806295,2	K562	blood:
11	chr6:26198540..26201852-chr6:27803216..27805609,3	MCF-7	breast:
12	chr6:27447703..27449538-chr6:27803629..27805992,2	K562	blood:
13	chr12:131486977..131489176-chr6:27802515..27804540,2	MCF-7	breast:
14	chr6:27599473..27601723-chr6:27802439..27805045,2	K562	blood:
15	chr6:27802664..27806163-chr6:28103303..28107418,3	K562	blood:
16	chr6:27802790..27806364-chr6:28301138..28304856,3	K562	blood:
17	chr6:27803974..27806831-chr6:28047434..28050953,3	K562	blood:
18	chr6:27111071..27119431-chr6:27801399..27810552,22	K562	blood:
19	chr6:26154851..26161490-chr6:27803982..27809302,10	MCF-7	breast:
20	chr6:26030223..26032455-chr6:27803494..27806163,2	MCF-7	breast:
21	chr6:27113200..27117534-chr6:27802228..27806893,11	MCF-7	breast:
22	chr6:27792916..27793498-chr6:27803944..27804589,2	K562	blood:
23	chr6:27447039..27449538-chr6:27803021..27805992,2	K562	blood:

No data

Variant related genes	Relation type
HIST1H4K	TF binding region
HIST1H2BN	TF binding region
ENSG00000196787	Chromatin interaction
ENSG00000197903	Chromatin interaction
ENSG00000235109	Chromatin interaction
ENSG00000197279	Chromatin interaction
ENSG00000184825	Chromatin interaction
ENSG00000269293	Chromatin interaction
ENSG00000198339	Chromatin interaction
ENSG00000196176	Chromatin interaction
ENSG00000265565	Chromatin interaction
ENSG00000168298	Chromatin interaction
ENSG00000217275	Chromatin interaction
ENSG00000197409	Chromatin interaction
ENSG00000124635	Chromatin interaction
ENSG00000158373	Chromatin interaction
ENSG00000111452	Chromatin interaction
ENSG00000197846	Chromatin interaction
ENSG00000196866	Chromatin interaction
ENSG00000261839	Chromatin interaction
ENSG00000124693	Chromatin interaction
ENSG00000198366	Chromatin interaction
ENSG00000137259	Chromatin interaction
ENSG00000272009	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs156741	1.00[TSI][hapmap]
rs156742	1.00[TSI][hapmap]
rs16867901	1.00[MEX][hapmap];1.00[TSI][hapmap]
rs16867911	1.00[TSI][hapmap]
rs169263	1.00[TSI][hapmap]
rs175597	0.91[MKK][hapmap];0.82[YRI][hapmap]
rs187995	1.00[EUR][1000 genomes]
rs200470	0.83[LWK][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs200472	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs200484	0.88[MKK][hapmap]
rs200487	1.00[ASW][hapmap];0.80[LWK][hapmap];0.93[YRI][hapmap]
rs200501	0.88[MKK][hapmap]
rs200947	1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs200948	0.91[MKK][hapmap];0.88[YRI][hapmap]
rs200954	0.82[YRI][hapmap]
rs200955	1.00[ASW][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs200959	0.84[ASW][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];1.00[EUR][1000 genomes]
rs200965	0.88[YRI][hapmap]
rs200970	1.00[TSI][hapmap]
rs200977	0.82[YRI][hapmap]
rs200982	1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs200984	1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs200989	0.91[MKK][hapmap];0.82[YRI][hapmap]
rs201003	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2747054	0.88[MKK][hapmap]
rs276364	1.00[TSI][hapmap]
rs401763	0.80[MKK][hapmap]
rs56342784	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59716769	1.00[EUR][1000 genomes]
rs7740062	1.00[EUR][1000 genomes]
rs9295739	1.00[MEX][hapmap];1.00[TSI][hapmap]
rs9468198	1.00[EUR][1000 genomes]
rs9468205	1.00[EUR][1000 genomes]
rs9468228	0.89[AMR][1000 genomes];1.00[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	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

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs201005	CRX	trans	brain	seeQTL
rs201005	TTR	trans	brain	seeQTL
rs201005	LRTM1	trans	brain	seeQTL
rs201005	GUCA1C	trans	brain	seeQTL
rs201005	ASMT	trans	brain	seeQTL
rs201005	PDE6H	trans	brain	seeQTL
rs201005	Hs.158943	cis	multi-tissue	Pritchard
rs201005	EMP1	trans	brain	seeQTL
rs201005	SH2D2A	trans	brain	seeQTL
rs201005	SLC5A7	trans	brain	seeQTL
rs201005	OTX2	trans	brain	seeQTL

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:27799000-27804200	Weak transcription	Spleen	Spleen
2	chr6:27799000-27804400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr6:27799000-27804600	Weak transcription	Lung	lung
4	chr6:27799000-27804600	Weak transcription	Ovary	ovary
5	chr6:27799000-27804600	Weak transcription	Pancreas	Pancrea
6	chr6:27799200-27804200	Weak transcription	Small Intestine	intestine
7	chr6:27799400-27804600	Weak transcription	Left Ventricle	heart
8	chr6:27799600-27804200	Weak transcription	Right Ventricle	heart
9	chr6:27799800-27804200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr6:27799800-27804200	Weak transcription	Primary T cells fromperipheralblood	blood
11	chr6:27799800-27804200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr6:27799800-27804200	Weak transcription	Fetal Muscle Trunk	muscle
13	chr6:27799800-27804400	Weak transcription	Placenta	Placenta
14	chr6:27800200-27804200	Weak transcription	Fetal Stomach	stomach
15	chr6:27801400-27804200	Enhancers	Primary T helper naive cells from peripheral blood	blood
16	chr6:27802000-27804600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr6:27802600-27804200	Enhancers	Fetal Intestine Small	intestine
18	chr6:27802600-27805800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr6:27802800-27804200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
20	chr6:27802800-27805000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr6:27802800-27808200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr6:27803000-27804200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
23	chr6:27803200-27804200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr6:27803200-27804200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr6:27803200-27804200	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr6:27803200-27804600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr6:27803200-27807400	Active TSS	K562	blood
28	chr6:27803200-27807600	Active TSS	Fetal Thymus	thymus
29	chr6:27803200-27808200	Active TSS	HUES48 Cell Line	embryonic stem cell
30	chr6:27803400-27808000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
31	chr6:27803400-27808400	Active TSS	GM12878-XiMat	blood
32	chr6:27803600-27804600	Flanking Active TSS	Primary T cells from cord blood	blood
33	chr6:27803600-27804600	Flanking Active TSS	Fetal Brain Female	brain
34	chr6:27803600-27804800	Flanking Active TSS	NH-A	brain
35	chr6:27803600-27805000	Flanking Active TSS	Dnd41	blood
36	chr6:27803800-27804200	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
37	chr6:27803800-27804200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
38	chr6:27803800-27804200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr6:27803800-27804200	Enhancers	Fetal Brain Male	brain
40	chr6:27803800-27804200	Enhancers	Skeletal Muscle Female	skeletal muscle
41	chr6:27803800-27804200	Enhancers	Stomach Mucosa	stomach
42	chr6:27803800-27804200	Flanking Active TSS	A549	lung
43	chr6:27803800-27804200	Enhancers	HUVEC	blood vessel
44	chr6:27803800-27804200	Active TSS	Osteobl	bone
45	chr6:27803800-27804400	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr6:27803800-27804400	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
47	chr6:27803800-27804400	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
48	chr6:27803800-27804400	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
49	chr6:27803800-27804400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr6:27803800-27804400	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links