Variant report

Variant	rs11895188
Chromosome Location	chr2:209130114-209130115
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:154)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:154 , 50 per page) page: 1 2 3 4

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:209130030-209130468	PFSK-1	brain:	n/a	n/a
2	MBD4	chr2:209129927-209131651	HepG2	liver:	n/a	n/a
3	USF1	chr2:209130076-209131203	ECC-1	luminal epithelium:	n/a	n/a
4	TBL1XR1	chr2:209129765-209131669	GM12878	blood:	n/a	n/a
5	POLR2A	chr2:209130039-209131427	K562	blood:	n/a	n/a
6	MAX	chr2:209130016-209131566	ECC-1	luminal epithelium:	n/a	chr2:209130353-209130362
7	MYC	chr2:209129863-209131263	K562	blood:	n/a	chr2:209130353-209130362
8	GATA1	chr2:209129668-209131288	K562	blood:	n/a	chr2:209130018-209130025 chr2:209130324-209130332
9	POLR2A	chr2:209129927-209131567	GM12892	blood:	n/a	n/a
10	POLR2A	chr2:209129919-209131492	GM12878	blood:	n/a	n/a
11	SP1	chr2:209129960-209131238	HCT-116	colon:	n/a	chr2:209130960-209130973 chr2:209130951-209130963
12	PAX5	chr2:209130108-209130407	GM12878	blood:	n/a	n/a
13	POLR2A	chr2:209130091-209130445	GM12891	blood:	n/a	n/a
14	POLR2A	chr2:209129908-209131339	ProgFib	skin:	n/a	n/a
15	POLR2A	chr2:209129665-209132065	GM12891	blood:	n/a	n/a
16	POLR2A	chr2:209130046-209131501	GM15510	blood:	n/a	n/a
17	POLR2A	chr2:209130054-209131410	HepG2	liver:	n/a	n/a
18	POLR2A	chr2:209130035-209131391	GM12891	blood:	n/a	n/a
19	CEBPB	chr2:209130033-209131096	GM12878	blood:	n/a	n/a
20	FOXM1	chr2:209130035-209131509	GM12878	blood:	n/a	n/a
21	POLR2A	chr2:209130056-209131196	K562	blood:	n/a	n/a
22	POLR2A	chr2:209130020-209130351	ECC-1	luminal epithelium:	n/a	n/a
23	MAFK	chr2:209129926-209131045	HepG2	liver:	n/a	n/a
24	MYBL2	chr2:209129979-209131322	HepG2	liver:	n/a	n/a
25	NFIC	chr2:209129999-209131096	HepG2	liver:	n/a	n/a
26	HEY1	chr2:209130080-209130358	K562	blood:	n/a	n/a
27	POLR2A	chr2:209130085-209131198	HCT-116	colon:	n/a	n/a
28	POLR2A	chr2:209129977-209130443	GM12891	blood:	n/a	n/a
29	POLR2A	chr2:209129750-209131632	GM12892	blood:	n/a	n/a
30	MAX	chr2:209129806-209131369	A549	lung:	n/a	chr2:209130353-209130362
31	POLR2A	chr2:209129719-209131530	GM19099	blood:	n/a	n/a
32	POLR2A	chr2:209129898-209131869	GM12878	blood:	n/a	n/a
33	USF2	chr2:209129894-209131003	HepG2	liver:	n/a	n/a
34	POLR2A	chr2:209129957-209131634	GM12878	blood:	n/a	n/a
35	TAF1	chr2:209130055-209130516	GM12878	blood:	n/a	n/a
36	POLR2A	chr2:209129772-209131636	NB4	blood:	n/a	n/a
37	POLR2A	chr2:209130069-209131496	GM10847	blood:	n/a	n/a
38	MAZ	chr2:209130094-209131810	GM12878	blood:	n/a	chr2:209130353-209130362
39	EP300	chr2:209130020-209131133	K562	blood:	n/a	n/a
40	TBP	chr2:209130057-209131721	GM12878	blood:	n/a	n/a
41	POLR2A	chr2:209130101-209130372	H1-hESC	embryonic stem cell:	n/a	n/a
42	TAF1	chr2:209130094-209130352	GM12891	blood:	n/a	n/a
43	WRNIP1	chr2:209129994-209131685	GM12878	blood:	n/a	n/a
44	POLR2A	chr2:209130075-209131225	SK-N-SH	brain:	n/a	n/a
45	POLR2A	chr2:209130049-209131250	K562	blood:	n/a	n/a
46	STAT5A	chr2:209130066-209131368	GM12878	blood:	n/a	chr2:209130796-209130805 chr2:209130797-209130806 chr2:209130967-209130979
47	YY1	chr2:209130060-209130399	GM12878	blood:	n/a	n/a
48	POLR2A	chr2:209130052-209130414	HepG2	liver:	n/a	n/a
49	POLR2A	chr2:209129999-209131293	HUVEC	blood vessel:	n/a	n/a
50	POLR2A	chr2:209130053-209131241	GM12891	blood:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:208393863..208396191-chr2:209128319..209130637,2	K562	blood:
2	chr2:209123964..209126958-chr2:209128019..209130689,2	K562	blood:
3	chr2:209129671..209132812-chr2:209132994..209136144,5	MCF-7	breast:
4	chr2:209128359..209130743-chr2:209169171..209171063,2	K562	blood:
5	chr2:209116323..209122695-chr2:209127326..209132568,14	K562	blood:
6	chr2:209119923..209123053-chr2:209129009..209130826,3	MCF-7	breast:
7	chr2:209116323..209123332-chr2:209127326..209134005,17	K562	blood:
8	chr2:209129669..209131681-chr2:209132251..209135245,2	K562	blood:
9	chr2:209117138..209121626-chr2:209129108..209132782,7	MCF-7	breast:

No data

Variant related genes	Relation type
PIKFYVE	TF binding region
ENSG00000231908	Chromatin interaction
ENSG00000228380	Chromatin interaction
ENSG00000118260	Chromatin interaction
ENSG00000138413	Chromatin interaction
ENSG00000223725	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10174541	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10186350	0.80[CEU][hapmap];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10194539	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10198535	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10202116	1.00[ASN][1000 genomes]
rs10497897	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10497898	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10497901	1.00[YRI][hapmap]
rs11538998	1.00[ASW][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs11554137	1.00[ASN][1000 genomes]
rs11685614	1.00[ASN][1000 genomes]
rs11885913	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11898653	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11901959	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11902124	1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap]
rs12475932	0.89[CEU][hapmap];1.00[CHD][hapmap]
rs12694100	0.91[EUR][1000 genomes]
rs12694101	0.96[EUR][1000 genomes]
rs13412043	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1347664	1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap]
rs1437413	1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap]
rs16841224	0.90[GIH][hapmap];0.94[LWK][hapmap];0.88[MEX][hapmap];1.00[YRI][hapmap]
rs16841236	1.00[CHD][hapmap];0.94[LWK][hapmap];0.88[MEX][hapmap];1.00[YRI][hapmap]
rs17699838	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs17700235	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs1816612	1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap]
rs1866046	0.84[ASW][hapmap];0.89[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap];0.86[TSI][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs34218846	0.95[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs35293936	1.00[CHD][hapmap]
rs3928183	1.00[ASN][1000 genomes]
rs4673394	0.80[CEU][hapmap]
rs4675751	0.80[CEU][hapmap]
rs59522113	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59684347	1.00[ASN][1000 genomes]
rs6435435	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs66826643	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs66887797	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs67171462	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67202912	0.95[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6725418	0.82[GIH][hapmap];0.96[EUR][1000 genomes]
rs6725527	0.84[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs67581965	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67669827	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72976889	1.00[ASN][1000 genomes]
rs72989243	0.97[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73056463	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73070950	1.00[ASN][1000 genomes]
rs73070958	0.95[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs73070962	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7557303	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7563597	1.00[YRI][hapmap]
rs7564720	1.00[YRI][hapmap]
rs7609093	0.95[AFR][1000 genomes]
rs9646838	0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs999890	0.80[CEU][hapmap];1.00[CHD][hapmap];0.89[MEX][hapmap]
rs999891	0.80[CEU][hapmap];1.00[CHD][hapmap];0.89[MEX][hapmap]

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	nsv1010531	chr2:208610639-209176782	Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv536130	chr2:208610639-209176782	Weak transcription Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Active TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv534496	chr2:208814372-209302791	Strong transcription Active TSS Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
4	nsv834517	chr2:209006797-209170269	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
5	nsv584297	chr2:209020181-209316760	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 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	chr2:209129600-209130200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr2:209129600-209130200	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr2:209129600-209130200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr2:209129600-209130200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr2:209129600-209130200	Enhancers	Placenta	Placenta
6	chr2:209129600-209130200	Enhancers	Lung	lung
7	chr2:209129600-209130200	Enhancers	Small Intestine	intestine
8	chr2:209129600-209130200	Flanking Active TSS	Dnd41	blood
9	chr2:209129600-209130400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
10	chr2:209129600-209130400	Flanking Active TSS	Stomach Smooth Muscle	stomach
11	chr2:209129600-209130600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr2:209129600-209130600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr2:209129600-209130800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr2:209129600-209130800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr2:209129600-209132000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
16	chr2:209129800-209130200	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
17	chr2:209129800-209130200	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
18	chr2:209129800-209130200	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
19	chr2:209129800-209130200	Enhancers	Primary neutrophils fromperipheralblood	blood
20	chr2:209129800-209130200	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr2:209129800-209130200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr2:209129800-209130200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr2:209129800-209130200	Flanking Active TSS	Brain Angular Gyrus	brain
24	chr2:209129800-209130200	Flanking Active TSS	Brain Anterior Caudate	brain
25	chr2:209129800-209130200	Flanking Active TSS	Brain Cingulate Gyrus	brain
26	chr2:209129800-209130200	Flanking Active TSS	Brain Germinal Matrix	brain
27	chr2:209129800-209130200	Flanking Active TSS	Brain Hippocampus Middle	brain
28	chr2:209129800-209130200	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
29	chr2:209129800-209130200	Flanking Active TSS	Brain Substantia Nigra	brain
30	chr2:209129800-209130200	Flanking Active TSS	Fetal Muscle Trunk	muscle
31	chr2:209129800-209130200	Flanking Active TSS	Left Ventricle	heart
32	chr2:209129800-209130200	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
33	chr2:209129800-209130200	Flanking Active TSS	Rectal Smooth Muscle	rectum
34	chr2:209129800-209130200	Flanking Active TSS	Thymus	Thymus
35	chr2:209129800-209130200	Flanking Active TSS	A549	lung
36	chr2:209129800-209130200	Flanking Active TSS	K562	blood
37	chr2:209129800-209130400	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
38	chr2:209129800-209130400	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
39	chr2:209129800-209130400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr2:209129800-209130400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
41	chr2:209129800-209130400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
42	chr2:209129800-209130400	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
43	chr2:209129800-209130400	Flanking Active TSS	Adipose Nuclei	Adipose
44	chr2:209129800-209130400	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
45	chr2:209129800-209130400	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
46	chr2:209129800-209130400	Flanking Active TSS	Fetal Brain Female	brain
47	chr2:209129800-209130400	Flanking Active TSS	Fetal Heart	heart
48	chr2:209129800-209130400	Flanking Active TSS	Fetal Kidney	kidney
49	chr2:209129800-209130400	Flanking Active TSS	Fetal Lung	lung
50	chr2:209129800-209130400	Flanking Active TSS	Fetal Stomach	stomach

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