Variant report

Variant	rs2276622
Chromosome Location	chr2:178977620-178977621
allele	C/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	POLR2A	chr2:178976719-178977714	PFSK-1	brain:	n/a	n/a
2	POLR2A	chr2:178976900-178977915	Raji	blood:	n/a	n/a
3	HCFC1	chr2:178976699-178977667	Hela-S3	cervix:	n/a	n/a
4	BHLHE40	chr2:178976965-178977652	GM12878	blood:	n/a	chr2:178977085-178977101
5	ELF1	chr2:178976652-178977683	MCF-7	breast:	n/a	chr2:178977166-178977175 chr2:178977162-178977175 chr2:178977165-178977174
6	POLR2A	chr2:178976868-178977943	HepG2	liver:	n/a	n/a
7	CBX3	chr2:178976748-178977833	HCT-116	colon:	n/a	n/a
8	POLR2A	chr2:178976872-178977644	GM12892	blood:	n/a	n/a
9	MAZ	chr2:178976878-178977828	K562	blood:	n/a	n/a
10	POLR2A	chr2:178976993-178977727	GM15510	blood:	n/a	n/a
11	CTCF	chr2:178976784-178977785	HCT-116	colon:	n/a	chr2:178977085-178977095 chr2:178977083-178977096 chr2:178977081-178977097 chr2:178977080-178977098
12	RELA	chr2:178976860-178977867	GM18951	blood:	n/a	n/a
13	POLR2A	chr2:178976891-178977631	GM12892	blood:	n/a	n/a
14	MXI1	chr2:178976593-178978663	SK-N-SH	brain:	n/a	n/a
15	REST	chr2:178976794-178977725	HepG2	liver:	n/a	chr2:178977695-178977705 chr2:178976979-178976986 chr2:178977639-178977652 chr2:178977135-178977144 chr2:178977103-178977113
16	MAZ	chr2:178976720-178978152	IMR90	lung:	n/a	n/a
17	MAX	chr2:178976924-178977884	H1-hESC	embryonic stem cell:	n/a	n/a
18	ELF1	chr2:178976841-178977929	GM12878	blood:	n/a	chr2:178977166-178977175 chr2:178977162-178977175 chr2:178977817-178977829 chr2:178977165-178977174
19	GATA2	chr2:178976656-178977628	SH-SY5Y	brain:	n/a	n/a
20	REST	chr2:178976711-178978040	H1-neurons	neurons:	n/a	chr2:178977695-178977705 chr2:178976979-178976986 chr2:178977639-178977652 chr2:178977135-178977144 chr2:178977103-178977113
21	E2F6	chr2:178976907-178977807	K562	blood:	n/a	chr2:178977143-178977153
22	UBTF	chr2:178976861-178977985	K562	blood:	n/a	n/a
23	TAF1	chr2:178976823-178977673	ECC-1	luminal epithelium:	n/a	n/a
24	HDAC2	chr2:178976803-178977698	MCF-7	breast:	n/a	n/a
25	TFAP2C	chr2:178976659-178977802	Hela-S3	cervix:	n/a	chr2:178976986-178977001 chr2:178977594-178977609
26	UBTF	chr2:178976965-178977926	K562	blood:	n/a	n/a
27	KAP1	chr2:178976648-178977676	HEK293	kidney:	n/a	n/a
28	MAX	chr2:178976870-178977929	K562	blood:	n/a	n/a
29	TCF12	chr2:178976787-178977812	ECC-1	luminal epithelium:	n/a	chr2:178977636-178977646
30	GABPA	chr2:178976636-178977813	MCF-7	breast:	n/a	n/a
31	TAF1	chr2:178976828-178977659	A549	lung:	n/a	n/a
32	SIN3AK20	chr2:178976832-178977719	A549	lung:	n/a	n/a
33	CCNT2	chr2:178976937-178977633	K562	blood:	n/a	n/a
34	YY1	chr2:178976923-178977685	K562	blood:	n/a	n/a
35	ELF1	chr2:178976847-178977683	K562	blood:	n/a	chr2:178977166-178977175 chr2:178977162-178977175 chr2:178977165-178977174
36	REST	chr2:178976842-178977639	MCF-7	breast:	n/a	chr2:178976979-178976986 chr2:178977135-178977144 chr2:178977103-178977113
37	MTA3	chr2:178976861-178977704	GM12878	blood:	n/a	n/a
38	POLR2A	chr2:178976855-178977795	GM19193	blood:	n/a	n/a
39	POLR2A	chr2:178976901-178977769	K562	blood:	n/a	n/a
40	POLR2A	chr2:178977000-178977761	GM12878	blood:	n/a	n/a
41	ZNF143	chr2:178976899-178977647	GM12878	blood:	n/a	chr2:178977089-178977099
42	ZNF143	chr2:178976879-178977638	H1-hESC	embryonic stem cell:	n/a	chr2:178977089-178977099
43	TAF1	chr2:178976884-178977650	H1-neurons	neurons:	n/a	n/a
44	SIN3A	chr2:178976882-178978017	H1-hESC	embryonic stem cell:	n/a	chr2:178977694-178977702 chr2:178977695-178977704 chr2:178977639-178977652 chr2:178977138-178977147 chr2:178977131-178977144
45	SIN3A	chr2:178977000-178977708	GM12878	blood:	n/a	chr2:178977694-178977702 chr2:178977695-178977704 chr2:178977639-178977652 chr2:178977138-178977147 chr2:178977131-178977144
46	CTCF	chr2:178977620-178977770	GM12864	blood:	n/a	n/a
47	TCF7L2	chr2:178976881-178977813	Hela-S3	cervix:	n/a	n/a
48	POLR2A	chr2:178976912-178977835	PBDE	blood:	n/a	n/a
49	POLR2A	chr2:178976943-178977872	A549	lung:	n/a	n/a
50	REST	chr2:178977521-178977819	H1-hESC	embryonic stem cell:	n/a	chr2:178977695-178977705 chr2:178977639-178977652

No.	Distal block	Cell Line	Cell type
1	chr2:178970656..178974678-chr2:178975520..178979270,3	K562	blood:
2	chr2:178974133..178981122-chr2:179276785..179281060,9	K562	blood:
3	chr2:178977351..178979746-chr2:178983845..178986068,3	K562	blood:
4	chr2:178976808..178978488-chr2:179342162..179344754,2	MCF-7	breast:
5	chr2:178977222..178979193-chr2:179277270..179279929,2	MCF-7	breast:
6	chr2:178975761..178978600-chr2:179056476..179059620,3	K562	blood:
7	chr2:178975067..178978289-chr2:179058254..179060575,4	MCF-7	breast:
8	chr2:178974707..178979925-chr2:179277151..179280371,6	K562	blood:
9	chr2:178972756..178975132-chr2:178975866..178978416,2	MCF-7	breast:
10	chr2:178976079..178979038-chr2:178986555..178992721,6	MCF-7	breast:
11	chr2:178976973..178979935-chr2:178988410..178990810,2	K562	blood:
12	chr2:178976419..178978821-chr2:179313368..179316809,4	K562	blood:

Variant related genes	Relation type
PDE11A	TF binding region
ENSG00000180228	Chromatin interaction
ENSG00000079150	Chromatin interaction
ENSG00000223960	Chromatin interaction
ENSG00000128655	Chromatin interaction
ENSG00000204311	Chromatin interaction
ENSG00000155636	Chromatin interaction
ENSG00000079156	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs1025446	0.85[JPT][hapmap]
rs12613853	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.82[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12617847	0.95[CHB][hapmap];0.86[JPT][hapmap];0.94[ASN][1000 genomes]
rs12619532	0.91[CHB][hapmap];0.85[JPT][hapmap];0.93[ASN][1000 genomes]
rs13005772	0.81[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs13006877	0.90[JPT][hapmap]
rs1435572	0.91[CHB][hapmap];0.85[JPT][hapmap];0.91[ASN][1000 genomes]
rs16866111	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs16866116	1.00[CHB][hapmap];0.90[JPT][hapmap];0.91[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs16866118	0.91[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs2366366	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs334062	0.85[JPT][hapmap]
rs334068	0.85[JPT][hapmap]
rs62176035	0.94[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs6705312	0.91[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs6753254	0.94[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs7564892	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][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	nsv1009312	chr2:178924318-179215566	Weak transcription Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv536057	chr2:178924318-179215566	Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Enhancers Flanking Active 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	11 gene(s)	inside rSNPs	diseases
3	nsv583739	chr2:178942302-178993562	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv518790	chr2:178963445-179000291	Weak transcription Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv875452	chr2:178963445-179167766	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 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	chr2:178976600-178977800	Active TSS	Primary T regulatory cells fromperipheralblood	blood
2	chr2:178976600-178978000	Active TSS	Lung	lung
3	chr2:178976800-178977800	Active TSS	Primary hematopoietic stem cells short term culture	blood
4	chr2:178976800-178977800	Active TSS	Brain Angular Gyrus	brain
5	chr2:178976800-178977800	Active TSS	Osteobl	bone
6	chr2:178976800-178978000	Active TSS	HUES64 Cell Line	embryonic stem cell
7	chr2:178976800-178978000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr2:178976800-178978000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr2:178976800-178978000	Active TSS	Colon Smooth Muscle	Colon
10	chr2:178976800-178978000	Active TSS	Duodenum Mucosa	Duodenum
11	chr2:178976800-178978000	Active TSS	Fetal Brain Female	brain
12	chr2:178976800-178978000	Active TSS	Fetal Lung	lung
13	chr2:178976800-178978000	Active TSS	Pancreas	Pancrea
14	chr2:178976800-178978200	Active TSS	H9 Cell Line	embryonic stem cell
15	chr2:178976800-178978200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr2:178976800-178978200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr2:178976800-178978200	Active TSS	iPS-20b Cell Line	embryonic stem cell
18	chr2:178976800-178978200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
19	chr2:178976800-178978200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr2:178976800-178978200	Active TSS	Brain Cingulate Gyrus	brain
21	chr2:178976800-178978200	Active TSS	Brain Hippocampus Middle	brain
22	chr2:178976800-178978200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
23	chr2:178976800-178978200	Active TSS	Fetal Intestine Small	intestine
24	chr2:178976800-178978200	Active TSS	Fetal Thymus	thymus
25	chr2:178976800-178978200	Active TSS	Rectal Mucosa Donor 29	rectum
26	chr2:178976800-178978200	Active TSS	Rectal Smooth Muscle	rectum
27	chr2:178976800-178978200	Active TSS	Thymus	Thymus
28	chr2:178976800-178978200	Active TSS	HSMM	muscle
29	chr2:178976800-178978200	Active TSS	HSMMtube	muscle
30	chr2:178976800-178978400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr2:178976800-178978600	Flanking Active TSS	Stomach Smooth Muscle	stomach
32	chr2:178977000-178977800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr2:178977000-178977800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
34	chr2:178977000-178977800	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
35	chr2:178977000-178977800	Active TSS	Pancreatic Islets	Pancreatic Islet
36	chr2:178977000-178977800	Active TSS	Placenta Amnion	Placenta Amnion
37	chr2:178977000-178977800	Active TSS	HUVEC	blood vessel
38	chr2:178977000-178977800	Active TSS	K562	blood
39	chr2:178977000-178978000	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr2:178977000-178978000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr2:178977000-178978000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr2:178977000-178978000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr2:178977000-178978000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr2:178977000-178978000	Active TSS	Primary T cells from cord blood	blood
45	chr2:178977000-178978000	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
46	chr2:178977000-178978000	Active TSS	Primary T helper cells PMA-I stimulated	--
47	chr2:178977000-178978000	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr2:178977000-178978000	Active TSS	Muscle Satellite Cultured Cells	--
49	chr2:178977000-178978000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr2:178977000-178978000	Active TSS	Brain Anterior Caudate	brain

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