Variant report

Variant	rs2230858
Chromosome Location	chr4:87968524-87968525
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:6)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:6 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr4:87967171-87970425	K562	blood:	n/a	n/a
2	CEBPB	chr4:87968432-87968578	K562	blood:	n/a	n/a
3	CEBPB	chr4:87968516-87968622	HepG2	liver:	n/a	n/a
4	POLR2A	chr4:87968041-87968604	GM12878	blood:	n/a	n/a
5	USF2	chr4:87968052-87968830	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr4:87967868-87968731	GM12878	blood:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:87960365..87962821-chr4:87965345..87969600,5	K562	blood:
2	chr4:87964446..87966356-chr4:87966393..87968677,2	MCF-7	breast:
3	chr4:87966822..87969393-chr4:87974722..87976813,3	K562	blood:
4	chr4:87965831..87967908-chr4:87968487..87970739,2	MCF-7	breast:
5	chr4:87854791..87857074-chr4:87968149..87971029,2	K562	blood:
6	chr4:87963142..87968842-chr4:87969641..87976222,9	K562	blood:

No data

Variant related genes	Relation type
AFF1	TF binding region
ENSG00000163633	Chromatin interaction
ENSG00000172493	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10003331	0.95[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10015544	1.00[ASN][1000 genomes]
rs10022825	1.00[ASN][1000 genomes]
rs10028134	1.00[CEU][hapmap]
rs10032200	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10050309	1.00[CEU][hapmap];0.94[YRI][hapmap];0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs1037813	1.00[ASN][1000 genomes]
rs12508231	1.00[ASN][1000 genomes]
rs13103234	1.00[ASN][1000 genomes]
rs13108043	1.00[ASN][1000 genomes]
rs13134084	1.00[ASN][1000 genomes]
rs17012304	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17030453	1.00[ASN][1000 genomes]
rs17604937	1.00[ASN][1000 genomes]
rs17668731	1.00[ASN][1000 genomes]
rs17668952	1.00[ASN][1000 genomes]
rs17703261	1.00[ASN][1000 genomes]
rs28495374	1.00[ASN][1000 genomes]
rs28667805	0.82[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs28791499	1.00[ASN][1000 genomes]
rs35658582	1.00[ASN][1000 genomes]
rs366327	1.00[ASN][1000 genomes]
rs56656813	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58478399	1.00[ASN][1000 genomes]
rs62306540	1.00[ASN][1000 genomes]
rs6822384	1.00[ASN][1000 genomes]
rs6846352	1.00[ASN][1000 genomes]
rs71607404	1.00[ASN][1000 genomes]
rs72877916	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs72877918	0.82[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7664479	1.00[ASN][1000 genomes]
rs7668285	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009937	chr4:87795314-88008345	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
2	nsv999176	chr4:87869996-88098136	Strong transcription Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	nsv998335	chr4:87869996-88104414	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv1001017	chr4:87872160-88087003	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
5	nsv537166	chr4:87872160-88087003	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
6	nsv999098	chr4:87899091-88016048	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
7	nsv537167	chr4:87899091-88016048	Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
8	nsv997750	chr4:87933945-88264127	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
9	nsv879525	chr4:87964363-88033352	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:87960400-87975400	Weak transcription	Brain Germinal Matrix	brain
2	chr4:87961000-87979200	Weak transcription	HSMMtube	muscle
3	chr4:87963200-87982200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr4:87964600-87995000	Weak transcription	Hela-S3	cervix
5	chr4:87964800-87979200	Weak transcription	A549	lung
6	chr4:87966200-87969800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr4:87966200-87979200	Weak transcription	NH-A	brain
8	chr4:87966400-87969800	Strong transcription	GM12878-XiMat	blood
9	chr4:87967000-87968800	Strong transcription	HMEC	breast
10	chr4:87967000-87968800	Strong transcription	NHEK	skin
11	chr4:87967000-87969800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr4:87967000-87970600	Genic enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr4:87967000-87971000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr4:87967000-87975000	Strong transcription	Dnd41	blood
15	chr4:87967200-87968600	Genic enhancers	Placenta	Placenta
16	chr4:87967200-87968600	Enhancers	Right Atrium	heart
17	chr4:87967200-87968800	Strong transcription	HUES48 Cell Line	embryonic stem cell
18	chr4:87967200-87968800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr4:87967200-87968800	Strong transcription	Thymus	Thymus
20	chr4:87967200-87969200	Strong transcription	Primary T helper cells PMA-I stimulated	--
21	chr4:87967200-87969200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr4:87967200-87969400	Strong transcription	HUES64 Cell Line	embryonic stem cell
23	chr4:87967200-87969400	Strong transcription	Rectal Mucosa Donor 29	rectum
24	chr4:87967200-87969600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr4:87967200-87969800	Weak transcription	Brain Angular Gyrus	brain
26	chr4:87967200-87971200	Strong transcription	Primary B cells from peripheral blood	blood
27	chr4:87967400-87969200	Strong transcription	Primary T helper cells fromperipheralblood	blood
28	chr4:87967400-87969600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
29	chr4:87967400-87969800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr4:87967400-87969800	Strong transcription	K562	blood
31	chr4:87967400-87970000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr4:87967400-87970000	Strong transcription	Rectal Mucosa Donor 31	rectum
33	chr4:87967400-87970200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
34	chr4:87967400-87970800	Strong transcription	Fetal Thymus	thymus
35	chr4:87967400-87973000	Strong transcription	Primary T cells fromperipheralblood	blood
36	chr4:87967600-87968600	Strong transcription	H1 Cell Line	embryonic stem cell
37	chr4:87967600-87968600	Strong transcription	H9 Cell Line	embryonic stem cell
38	chr4:87967600-87969000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
39	chr4:87967600-87969000	Strong transcription	Primary T cells from cord blood	blood
40	chr4:87967600-87969000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr4:87967600-87969200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr4:87967600-87969400	Weak transcription	Fetal Heart	heart
43	chr4:87967600-87969800	Weak transcription	Brain Substantia Nigra	brain
44	chr4:87967600-87970200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
45	chr4:87967600-87970200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr4:87967600-87971000	Strong transcription	Sigmoid Colon	Sigmoid Colon
47	chr4:87967600-87975000	Weak transcription	Stomach Mucosa	stomach
48	chr4:87967800-87968600	Strong transcription	iPS-15b Cell Line	embryonic stem cell
49	chr4:87967800-87968600	Strong transcription	Fetal Muscle Trunk	muscle
50	chr4:87967800-87968800	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell

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