Variant report

Variant	rs3828305
Chromosome Location	chr2:234246994-234246995
allele	C/T
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	GATA3	chr2:234246416-234247112	SH-SY5Y	brain:	n/a	n/a
2	USF1	chr2:234246839-234247023	SK-N-SH_RA	brain:	n/a	n/a
3	GATA3	chr2:234246659-234247212	MCF-7	breast:	n/a	n/a
4	RAD21	chr2:234246711-234247035	MCF-7	breast:	n/a	n/a
5	CTCF	chr2:234246860-234247010	BE2_C	brain:	n/a	n/a
6	MAX	chr2:234246710-234247109	NB4	blood:	n/a	chr2:234246926-234246933 chr2:234246925-234246934
7	RAD21	chr2:234246803-234247076	SK-N-SH_RA	brain:	n/a	n/a
8	MXI1	chr2:234246353-234247286	SK-N-SH	brain:	n/a	n/a
9	GATA3	chr2:234246670-234247270	SK-N-SH	brain:	n/a	n/a
10	RCOR1	chr2:234246911-234247054	K562	blood:	n/a	n/a
11	GATA2	chr2:234246460-234247321	SH-SY5Y	brain:	n/a	n/a
12	CTCF	chr2:234246781-234247049	K562	blood:	n/a	n/a
13	CTCF	chr2:234246971-234246994	H1-hESC	embryonic stem cell:	n/a	n/a
14	MAZ	chr2:234246886-234247058	K562	blood:	n/a	chr2:234246926-234246933 chr2:234246925-234246934
15	MAX	chr2:234246725-234247141	MCF-7	breast:	n/a	chr2:234246926-234246933 chr2:234246925-234246934
16	GATA3	chr2:234246731-234247108	T-47D	breast:	n/a	n/a
17	MYC	chr2:234246756-234247131	NB4	blood:	n/a	chr2:234246926-234246933 chr2:234246925-234246934
18	GATA3	chr2:234246593-234247234	SK-N-SH	brain:	n/a	n/a
19	BHLHE40	chr2:234246726-234247173	K562	blood:	n/a	n/a
20	CTCF	chr2:234246751-234247024	K562	blood:	n/a	n/a
21	MAX	chr2:234246735-234247054	K562	blood:	n/a	chr2:234246926-234246933 chr2:234246925-234246934
22	CTCF	chr2:234246880-234247030	HBMEC	blood vessel:	n/a	n/a
23	MYC	chr2:234246864-234247116	K562	blood:	n/a	chr2:234246926-234246933 chr2:234246925-234246934
24	CTCF	chr2:234246860-234247010	WERI-Rb-1	eye:	n/a	n/a
25	USF1	chr2:234246772-234247099	SK-N-SH_RA	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:234159356..234161467-chr2:234246206..234249085,2	MCF-7	breast:
2	chr2:234245499..234247293-chr2:234261946..234264130,2	K562	blood:
3	chr2:234242293..234245038-chr2:234245423..234247780,3	MCF-7	breast:

Variant related genes	Relation type
SAG	TF binding region
ENSG00000243637	Chromatin interaction
ENSG00000085978	Chromatin interaction
ENSG00000259793	Chromatin interaction
ENSG00000130561	Chromatin interaction
ENSG00000077044	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1000141	0.89[ASW][hapmap];0.85[CEU][hapmap];0.83[CHB][hapmap];0.83[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1046974	0.87[CHB][hapmap];0.80[CHD][hapmap];0.88[JPT][hapmap];0.84[MEX][hapmap]
rs10803624	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10803625	0.86[ASN][1000 genomes]
rs11676156	0.95[ASN][1000 genomes]
rs11679046	0.95[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs11681192	0.95[ASN][1000 genomes]
rs11682579	0.95[ASN][1000 genomes]
rs12997325	0.81[EUR][1000 genomes]
rs13002340	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13003198	0.87[ASN][1000 genomes]
rs13014016	0.95[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap]
rs2241873	0.87[CHB][hapmap]
rs2289477	0.81[CHB][hapmap]
rs2304774	0.81[EUR][1000 genomes]
rs2304776	0.81[AMR][1000 genomes]
rs2879924	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2879925	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34595600	0.97[ASN][1000 genomes]
rs34891595	0.97[ASN][1000 genomes]
rs35480652	0.95[ASN][1000 genomes]
rs3792091	0.89[MEX][hapmap]
rs3792093	0.83[CHB][hapmap];0.80[CHD][hapmap];0.83[TSI][hapmap]
rs55991949	0.81[EUR][1000 genomes]
rs67399374	0.95[ASN][1000 genomes]
rs7423426	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs880114	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs880116	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv584699	chr2:234182240-234255547	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv584700	chr2:234199401-234364426	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv1002075	chr2:234225979-234277508	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv529419	chr2:234229606-234670426	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
5	nsv460135	chr2:234242347-234288048	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv584701	chr2:234242347-234288048	ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	nsv460136	chr2:234244395-234288048	Weak transcription Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
8	nsv584702	chr2:234244395-234288048	Flanking Active TSS Bivalent/Poised TSS Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3828305	ATG16L1	cis	cerebellum	SCAN
rs3828305	SCARNA5	cis	parietal	SCAN
rs3828305	SCARNA5	cis	cerebellum	SCAN
rs3828305	DGKD	cis	cerebellum	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:234237400-234249800	Enhancers	Primary B cells from peripheral blood	blood
2	chr2:234241000-234249600	Enhancers	Primary B cells from cord blood	blood
3	chr2:234243000-234247800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr2:234243600-234247000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr2:234244000-234247000	Weak transcription	Primary neutrophils fromperipheralblood	blood
6	chr2:234244000-234247400	Weak transcription	Spleen	Spleen
7	chr2:234244200-234247600	Weak transcription	GM12878-XiMat	blood
8	chr2:234244400-234247400	Enhancers	Rectal Mucosa Donor 31	rectum
9	chr2:234244600-234247400	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr2:234244600-234247600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
11	chr2:234244600-234257800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr2:234245600-234247600	Weak transcription	Small Intestine	intestine
13	chr2:234245800-234247200	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr2:234245800-234247600	Weak transcription	Duodenum Mucosa	Duodenum
15	chr2:234246000-234247200	Weak transcription	Fetal Intestine Small	intestine
16	chr2:234246000-234247600	Weak transcription	Fetal Intestine Large	intestine
17	chr2:234246200-234247200	Weak transcription	Colonic Mucosa	Colon
18	chr2:234246600-234247000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr2:234246600-234247200	Enhancers	Monocytes-CD14+_RO01746	blood
20	chr2:234246600-234247400	Enhancers	K562	blood
21	chr2:234246600-234249400	Enhancers	Primary monocytes fromperipheralblood	blood
22	chr2:234246800-234247000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
23	chr2:234246800-234247400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
24	chr2:234246800-234247400	Enhancers	Placenta	Placenta

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