Variant report

Variant	rs6429884
Chromosome Location	chr2:142225328-142225329
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:142224514..142226282-chr2:142227850..142230425,2	MCF-7	breast:
2	chr2:142223846..142226689-chr2:142887518..142889461,2	MCF-7	breast:
3	chr2:142225007..142227143-chr2:142273674..142276575,2	MCF-7	breast:
4	chr2:142223533..142226548-chr2:142266133..142269163,3	MCF-7	breast:
5	chr2:142152511..142154867-chr2:142224989..142226849,2	MCF-7	breast:
6	chr2:142224840..142226819-chr2:142260426..142263186,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000168702	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10182090	0.88[JPT][hapmap]
rs10184273	0.88[YRI][hapmap]
rs10188231	1.00[JPT][hapmap]
rs10204518	0.85[YRI][hapmap]
rs10496885	0.88[CHD][hapmap];1.00[JPT][hapmap]
rs10928103	0.93[JPT][hapmap]
rs10928104	0.93[JPT][hapmap]
rs11677045	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[MKK][hapmap];0.97[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12052672	0.88[JPT][hapmap]
rs12464897	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12470243	0.81[ASN][1000 genomes]
rs12472911	1.00[ASW][hapmap];0.80[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12618990	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13008033	0.88[JPT][hapmap]
rs13394458	0.93[JPT][hapmap]
rs13397685	0.84[JPT][hapmap]
rs13401279	0.88[JPT][hapmap]
rs13408702	0.93[JPT][hapmap]
rs13415966	0.93[JPT][hapmap]
rs1384660	1.00[JPT][hapmap]
rs1483144	0.81[CEU][hapmap]
rs1483149	0.82[JPT][hapmap]
rs17551974	0.88[JPT][hapmap]
rs35839910	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3935991	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3936044	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3936045	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4073067	0.93[JPT][hapmap]
rs4131524	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4264514	0.93[YRI][hapmap]
rs4335888	0.93[YRI][hapmap]
rs4401160	0.86[JPT][hapmap]
rs4416160	0.93[YRI][hapmap]
rs4446018	0.93[YRI][hapmap]
rs4446019	0.93[YRI][hapmap]
rs4531869	0.93[YRI][hapmap]
rs5012231	0.93[YRI][hapmap]
rs62166279	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6429886	0.93[YRI][hapmap]
rs6718919	0.85[YRI][hapmap]
rs6719026	0.93[YRI][hapmap]
rs6733981	0.93[YRI][hapmap]
rs6733988	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.88[JPT][hapmap];0.91[LWK][hapmap];0.88[MKK][hapmap];0.91[TSI][hapmap];0.93[YRI][hapmap]
rs7584391	0.88[JPT][hapmap]
rs9287318	0.89[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:26 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817518	chr2:141714174-142287302	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv583203	chr2:142055133-142378975	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	esv2759095	chr2:142071391-142245947	Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv875234	chr2:142156180-142254119	Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
5	nsv875236	chr2:142158967-142239599	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
6	nsv1009183	chr2:142165632-142234165	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
7	nsv1002208	chr2:142167237-142235308	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
8	nsv522093	chr2:142172366-142242597	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
9	nsv875237	chr2:142172366-142242597	Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
10	nsv875238	chr2:142180831-142242597	Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
11	esv34606	chr2:142181268-142239268	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
12	esv3693425	chr2:142184803-142239599	Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
13	nsv1004494	chr2:142185449-142240487	Enhancers ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
14	esv34823	chr2:142187268-142239268	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
15	nsv875239	chr2:142195346-142239599	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
16	esv2756949	chr2:142196123-142245947	Weak transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
17	nsv583205	chr2:142199421-142228509	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
18	nsv875240	chr2:142199421-142347455	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
19	nsv875241	chr2:142210946-142239599	Weak transcription Enhancers Flanking Active TSS Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
20	nsv875242	chr2:142216767-142242597	Enhancers Weak transcription Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
21	nsv583206	chr2:142219033-142234165	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
22	nsv875243	chr2:142219033-142259592	Enhancers Weak transcription Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
23	nsv516298	chr2:142220408-142226768	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
24	nsv960990	chr2:142221605-142225461	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
25	esv3383787	chr2:142223732-142225880	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
26	esv3420861	chr2:142224232-142225380	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6429884	HIST1H4E	trans	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:142221800-142225800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr2:142225000-142226000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
3	chr2:142225000-142227000	Enhancers	ES-I3 Cell Line	embryonic stem cell

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