Variant report

Variant	rs4894197
Chromosome Location	chr2:177628917-177628918
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	TCF12	chr2:177628824-177629204	GM12878	blood:	n/a	n/a
2	MAZ	chr2:177628862-177629118	GM12878	blood:	n/a	chr2:177628976-177628985 chr2:177628975-177628984
3	HDAC2	chr2:177628677-177629197	H1-hESC	embryonic stem cell:	n/a	n/a
4	ATF2	chr2:177628630-177629258	H1-hESC	embryonic stem cell:	n/a	n/a
5	TCF12	chr2:177628682-177629304	H1-hESC	embryonic stem cell:	n/a	n/a
6	TCF3	chr2:177628787-177629175	GM12878	blood:	n/a	n/a
7	YY1	chr2:177628703-177629230	H1-hESC	embryonic stem cell:	n/a	n/a
8	SP1	chr2:177628672-177629216	H1-hESC	embryonic stem cell:	n/a	chr2:177629069-177629083
9	TBP	chr2:177628681-177629065	H1-hESC	embryonic stem cell:	n/a	n/a
10	JUND	chr2:177628538-177629399	H1-hESC	embryonic stem cell:	n/a	chr2:177628976-177628984 chr2:177628975-177628985 chr2:177628975-177628984 chr2:177628979-177628991 chr2:177628976-177628983
11	SIN3A	chr2:177628540-177629179	H1-hESC	embryonic stem cell:	n/a	n/a
12	BATF	chr2:177628707-177629176	GM12878	blood:	n/a	chr2:177628977-177628987 chr2:177628972-177628983
13	NRF1	chr2:177628847-177628999	GM12878	blood:	n/a	n/a
14	CTBP2	chr2:177628692-177629231	H1-hESC	embryonic stem cell:	n/a	n/a
15	MAX	chr2:177628600-177629265	H1-hESC	embryonic stem cell:	n/a	chr2:177628976-177628985 chr2:177628975-177628984
16	RUNX3	chr2:177628790-177629194	GM12878	blood:	n/a	n/a
17	MAFK	chr2:177628531-177629445	H1-hESC	embryonic stem cell:	n/a	n/a
18	BACH1	chr2:177628663-177629142	H1-hESC	embryonic stem cell:	n/a	chr2:177628973-177628987
19	NANOG	chr2:177628815-177629139	H1-hESC	embryonic stem cell:	n/a	chr2:177629012-177629021
20	MAX	chr2:177628698-177629221	H1-hESC	embryonic stem cell:	n/a	chr2:177628976-177628985 chr2:177628975-177628984
21	JUND	chr2:177628714-177629203	H1-hESC	embryonic stem cell:	n/a	chr2:177628976-177628984 chr2:177628975-177628985 chr2:177628975-177628984 chr2:177628979-177628991 chr2:177628976-177628983
22	FOS	chr2:177628781-177629009	MCF10A-Er-Src	breast:	n/a	chr2:177628976-177628984 chr2:177628975-177628985 chr2:177628975-177628984 chr2:177628979-177628991 chr2:177628976-177628983
23	POLR2A	chr2:177628702-177629055	H1-hESC	embryonic stem cell:	n/a	n/a
24	TEAD4	chr2:177628667-177629185	H1-hESC	embryonic stem cell:	n/a	n/a
25	ATF2	chr2:177628674-177629170	H1-hESC	embryonic stem cell:	n/a	n/a
26	TEAD4	chr2:177628698-177629234	H1-hESC	embryonic stem cell:	n/a	n/a
27	SRF	chr2:177628774-177629138	H1-hESC	embryonic stem cell:	n/a	chr2:177628822-177628832
28	POLR2A	chr2:177628662-177629086	H1-hESC	embryonic stem cell:	n/a	n/a
29	EP300	chr2:177628726-177629274	H1-hESC	embryonic stem cell:	n/a	chr2:177628976-177628985 chr2:177628975-177628984
30	POU2F2	chr2:177628693-177629196	GM12891	blood:	n/a	chr2:177629012-177629020 chr2:177629011-177629020 chr2:177629010-177629020 chr2:177629009-177629021 chr2:177629007-177629025 chr2:177629011-177629022 chr2:177629009-177629023 chr2:177629010-177629020 chr2:177629006-177629027 chr2:177629012-177629019 chr2:177629008-177629023 chr2:177629011-177629021
31	YY1	chr2:177628783-177629159	H1-hESC	embryonic stem cell:	n/a	n/a
32	JUND	chr2:177628802-177629163	H1-hESC	embryonic stem cell:	n/a	chr2:177628976-177628984 chr2:177628975-177628985 chr2:177628975-177628984 chr2:177628979-177628991 chr2:177628976-177628983
33	POU5F1	chr2:177628623-177629213	H1-hESC	embryonic stem cell:	n/a	chr2:177629012-177629020 chr2:177629012-177629026 chr2:177629012-177629026
34	FOS	chr2:177628695-177628956	MCF10A-Er-Src	breast:	n/a	n/a
35	EBF1	chr2:177628837-177629224	GM12878	blood:	n/a	n/a
36	TCF12	chr2:177628793-177629174	GM12878	blood:	n/a	n/a
37	MAX	chr2:177628659-177629146	H1-hESC	embryonic stem cell:	n/a	chr2:177628976-177628985 chr2:177628975-177628984
38	MYC	chr2:177628871-177628936	MCF10A-Er-Src	breast:	n/a	n/a
39	JUN	chr2:177628796-177629153	H1-hESC	embryonic stem cell:	n/a	chr2:177628976-177628984 chr2:177628975-177628985 chr2:177628975-177628984 chr2:177628979-177628991 chr2:177628976-177628983
40	SP1	chr2:177628668-177629196	H1-hESC	embryonic stem cell:	n/a	chr2:177629069-177629083
41	TCF12	chr2:177628741-177629177	H1-hESC	embryonic stem cell:	n/a	n/a
42	BATF	chr2:177628764-177629146	GM12878	blood:	n/a	chr2:177628977-177628987 chr2:177628972-177628983
43	TCF3	chr2:177628624-177629240	GM12878	blood:	n/a	n/a
44	POU2F2	chr2:177628792-177629165	GM12878	blood:	n/a	chr2:177629012-177629020 chr2:177629011-177629020 chr2:177629010-177629020 chr2:177629009-177629021 chr2:177629007-177629025 chr2:177629011-177629022 chr2:177629009-177629023 chr2:177629010-177629020 chr2:177629006-177629027 chr2:177629012-177629019 chr2:177629008-177629023 chr2:177629011-177629021
45	POU2F2	chr2:177628717-177629207	GM12878	blood:	n/a	chr2:177629012-177629020 chr2:177629011-177629020 chr2:177629010-177629020 chr2:177629009-177629021 chr2:177629007-177629025 chr2:177629011-177629022 chr2:177629009-177629023 chr2:177629010-177629020 chr2:177629006-177629027 chr2:177629012-177629019 chr2:177629008-177629023 chr2:177629011-177629021
46	BCL11A	chr2:177628846-177629122	H1-hESC	embryonic stem cell:	n/a	chr2:177628975-177628984 chr2:177628976-177628985
47	CREB1	chr2:177628563-177629226	H1-hESC	embryonic stem cell:	n/a	n/a
48	IRF4	chr2:177628744-177629135	GM12878	blood:	n/a	n/a
49	EP300	chr2:177628862-177629140	GM12878	blood:	n/a	chr2:177628976-177628985 chr2:177628975-177628984
50	CHD2	chr2:177628775-177629306	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:177627395..177629802-chr2:177630789..177633436,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000230552	TF binding region
ENSG00000230552	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10930752	1.00[CEU][hapmap];0.82[CHB][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11889984	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[GIH][hapmap];0.86[JPT][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12467333	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12469087	0.83[CEU][hapmap];1.00[CHB][hapmap];0.94[TSI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12611718	0.82[CHB][hapmap];0.83[ASN][1000 genomes]
rs12616782	1.00[YRI][hapmap]
rs12618099	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs2221939	0.83[CEU][hapmap]
rs4021394	0.94[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4600700	1.00[CEU][hapmap];0.82[CHB][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4894198	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs4894200	1.00[CEU][hapmap];0.82[CHB][hapmap];0.84[GIH][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6706063	1.00[CEU][hapmap];0.93[GIH][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs6706426	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6714936	0.81[TSI][hapmap]
rs6758766	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[GIH][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv527737	chr2:177538266-177692572	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv583686	chr2:177538266-177692572	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv1006500	chr2:177548521-177707097	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv524841	chr2:177628258-177632714	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4894197	HOXD11	cis	cerebellum	SCAN
rs4894197	LOC100130691	cis	parietal	SCAN

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:177623400-177634400	Weak transcription	Right Atrium	heart
2	chr2:177627000-177629000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
3	chr2:177627000-177629200	Enhancers	iPS-18 Cell Line	embryonic stem cell
4	chr2:177627800-177629600	Enhancers	Brain Germinal Matrix	brain
5	chr2:177628000-177630600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr2:177628200-177629200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr2:177628200-177629400	Enhancers	Fetal Brain Female	brain
8	chr2:177628200-177629600	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
9	chr2:177628200-177629800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr2:177628400-177629000	Enhancers	Skeletal Muscle Female	skeletal muscle
11	chr2:177628400-177631000	Enhancers	H9 Cell Line	embryonic stem cell
12	chr2:177628600-177629000	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
13	chr2:177628600-177629000	Flanking Active TSS	GM12878-XiMat	blood
14	chr2:177628600-177629200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr2:177628600-177629200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr2:177628600-177629400	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
17	chr2:177628600-177631200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr2:177628800-177629000	Enhancers	H1 Cell Line	embryonic stem cell
19	chr2:177628800-177629000	Enhancers	Left Ventricle	heart
20	chr2:177628800-177629200	Enhancers	iPS-20b Cell Line	embryonic stem cell
21	chr2:177628800-177629200	Bivalent Enhancer	Fetal Brain Male	brain
22	chr2:177628800-177630400	Enhancers	Primary B cells from peripheral blood	blood
23	chr2:177628800-177630800	Enhancers	HUES64 Cell Line	embryonic stem cell
24	chr2:177628800-177631400	Enhancers	ES-I3 Cell Line	embryonic stem cell
25	chr2:177628800-177655400	Weak transcription	Ovary	ovary

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