Variant report

Variant	rs3828307
Chromosome Location	chr2:234244395-234244396
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:234238740..234240381-chr2:234244254..234246759,2	MCF-7	breast:
2	chr2:234243950..234246353-chr2:234247665..234249180,2	K562	blood:
3	chr2:234242293..234245038-chr2:234245423..234247780,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000130561	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1000548	0.82[CEU][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.87[TSI][hapmap];0.92[YRI][hapmap]
rs1046976	1.00[CHB][hapmap];0.80[GIH][hapmap]
rs10929178	1.00[CHB][hapmap]
rs11675254	1.00[CHB][hapmap]
rs11675858	1.00[CHB][hapmap]
rs11679064	0.82[CEU][hapmap]
rs11694406	1.00[CHB][hapmap]
rs11890330	0.82[CEU][hapmap]
rs11890449	0.82[CEU][hapmap]
rs3754595	1.00[CHB][hapmap]
rs3796090	1.00[CHB][hapmap]
rs3796092	1.00[CHB][hapmap]
rs3820744	1.00[CHB][hapmap]
rs56121794	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs57592542	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6431322	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6704644	1.00[CHB][hapmap]
rs6719241	0.82[CEU][hapmap];1.00[CHD][hapmap]
rs6746234	1.00[CHB][hapmap]
rs6748547	0.82[CEU][hapmap]
rs6753242	1.00[CHB][hapmap]
rs7564805	0.84[ASW][hapmap];0.82[CEU][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.87[TSI][hapmap];0.92[YRI][hapmap]
rs7565275	0.84[ASW][hapmap];0.82[CEU][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.87[TSI][hapmap];0.92[YRI][hapmap]
rs7587876	1.00[CHB][hapmap]
rs7598771	1.00[CHB][hapmap]

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

No data

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:234223600-234245400	Weak transcription	Pancreas	Pancrea
2	chr2:234237400-234249800	Enhancers	Primary B cells from peripheral blood	blood
3	chr2:234238400-234244600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
4	chr2:234238800-234246600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr2:234240200-234244400	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr2:234240200-234245400	Weak transcription	Colonic Mucosa	Colon
7	chr2:234240400-234244600	Enhancers	Primary T cells fromperipheralblood	blood
8	chr2:234240600-234244800	Enhancers	Primary T helper cells fromperipheralblood	blood
9	chr2:234240800-234244600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
10	chr2:234240800-234244600	Enhancers	Primary T helper cells PMA-I stimulated	--
11	chr2:234240800-234244800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
12	chr2:234240800-234246600	Weak transcription	K562	blood
13	chr2:234241000-234244600	Enhancers	Primary T killer memory cells from peripheral blood	blood
14	chr2:234241000-234245400	Weak transcription	Fetal Intestine Small	intestine
15	chr2:234241000-234249600	Enhancers	Primary B cells from cord blood	blood
16	chr2:234242800-234244600	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr2:234243000-234244600	Weak transcription	Duodenum Mucosa	Duodenum
18	chr2:234243000-234247800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr2:234243600-234244400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
20	chr2:234243600-234247000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
21	chr2:234244000-234244600	Enhancers	Sigmoid Colon	Sigmoid Colon
22	chr2:234244000-234246600	Weak transcription	Primary monocytes fromperipheralblood	blood
23	chr2:234244000-234246600	Weak transcription	Monocytes-CD14+_RO01746	blood
24	chr2:234244000-234247000	Weak transcription	Primary neutrophils fromperipheralblood	blood
25	chr2:234244000-234247400	Weak transcription	Spleen	Spleen
26	chr2:234244200-234245200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
27	chr2:234244200-234247600	Weak transcription	GM12878-XiMat	blood

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