Variant report

Variant	rs896
Chromosome Location	chr3:42578335-42578336
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:12)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:12 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr3:42578320-42578470	HMF	breast:	n/a	n/a
2	POLR2A	chr3:42578284-42578701	K562	blood:	n/a	n/a
3	RAD21	chr3:42577725-42578430	HCT-116	colon:	n/a	n/a
4	CTCF	chr3:42578320-42578470	HRPEpiC	eye:	n/a	n/a
5	POLR2A	chr3:42578140-42578372	H1-hESC	embryonic stem cell:	n/a	n/a
6	RAD21	chr3:42577967-42578357	MCF-7	breast:	n/a	n/a
7	HEY1	chr3:42578236-42578799	K562	blood:	n/a	n/a
8	RAD21	chr3:42577805-42578346	H1-hESC	embryonic stem cell:	n/a	n/a
9	RAD21	chr3:42577837-42578369	ECC-1	luminal epithelium:	n/a	n/a
10	CTCF	chr3:42577703-42578396	HCT-116	colon:	n/a	n/a
11	CTCF	chr3:42577865-42578458	A549	lung:	n/a	n/a
12	NR2F2	chr3:42577897-42578442	MCF-7	breast:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr3:42576192..42579713-chr3:42587519..42590896,6	K562	blood:
2	chr3:42575887..42578856-chr3:42582315..42584372,2	K562	blood:
3	chr3:42574066..42576478-chr3:42578308..42581345,3	K562	blood:
4	chr3:42485131..42485764-chr3:42577911..42578463,2	MCF-7	breast:
5	chr3:42568447..42571025-chr3:42577137..42580427,3	K562	blood:
6	chr3:42289147..42289923-chr3:42577661..42578535,2	K562	blood:

No data

Variant related genes	Relation type
VIPR1-AS1	TF binding region
ENSG00000232354	Chromatin interaction
ENSG00000114812	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs168207	0.91[ASW][hapmap];0.81[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];0.89[JPT][hapmap];0.96[MEX][hapmap];0.91[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs342511	0.89[LWK][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs8913	0.80[AMR][1000 genomes]
rs895	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];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs897	0.82[CEU][hapmap];0.92[GIH][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529987	chr3:41921995-42591771	Bivalent Enhancer Weak transcription Flanking Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv1005533	chr3:41953873-42596375	Enhancers Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	esv1804804	chr3:42515186-42582403	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	esv1814102	chr3:42539966-42582403	Flanking Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv1002944	chr3:42559762-42728909	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs896	ZNF197	cis	parietal	SCAN
rs896	MOBP	cis	parietal	SCAN

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:42547600-42579000	Weak transcription	Rectal Smooth Muscle	rectum
2	chr3:42552200-42581000	Weak transcription	Pancreas	Pancrea
3	chr3:42557800-42586000	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr3:42557800-42590400	Weak transcription	Aorta	Aorta
5	chr3:42558000-42585200	Weak transcription	Brain Hippocampus Middle	brain
6	chr3:42561000-42581000	Weak transcription	Gastric	stomach
7	chr3:42562400-42586800	Weak transcription	Small Intestine	intestine
8	chr3:42567600-42580200	Strong transcription	Fetal Intestine Small	intestine
9	chr3:42570000-42580800	Weak transcription	Colonic Mucosa	Colon
10	chr3:42571200-42581200	Weak transcription	Right Atrium	heart
11	chr3:42571800-42581600	Weak transcription	Liver	Liver
12	chr3:42571800-42586200	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr3:42572600-42578600	Genic enhancers	Monocytes-CD14+_RO01746	blood
14	chr3:42572800-42581000	Weak transcription	Right Ventricle	heart
15	chr3:42573800-42580800	Weak transcription	Stomach Mucosa	stomach
16	chr3:42574600-42585000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr3:42574800-42579800	Weak transcription	Duodenum Mucosa	Duodenum
18	chr3:42574800-42585600	Weak transcription	Brain Anterior Caudate	brain
19	chr3:42574800-42590200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr3:42575000-42579600	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr3:42575200-42589200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr3:42575200-42594400	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr3:42575600-42590000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr3:42575800-42581000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
25	chr3:42575800-42581400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
26	chr3:42576200-42580800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
27	chr3:42576200-42581200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
28	chr3:42576400-42578400	Enhancers	Primary T helper cells fromperipheralblood	blood
29	chr3:42576400-42578400	Weak transcription	Spleen	Spleen
30	chr3:42576400-42580600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr3:42576600-42578400	Enhancers	Primary monocytes fromperipheralblood	blood
32	chr3:42576600-42586000	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr3:42577200-42578400	Enhancers	HUES6 Cell Line	embryonic stem cell
34	chr3:42577200-42578400	Enhancers	iPS-18 Cell Line	embryonic stem cell
35	chr3:42577200-42581000	Weak transcription	Fetal Intestine Large	intestine
36	chr3:42577400-42578600	Genic enhancers	Primary T cells fromperipheralblood	blood
37	chr3:42577400-42581200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
38	chr3:42577400-42590800	Weak transcription	H9 Cell Line	embryonic stem cell
39	chr3:42577400-42592800	Weak transcription	HUES64 Cell Line	embryonic stem cell
40	chr3:42577600-42592000	Weak transcription	HUES48 Cell Line	embryonic stem cell
41	chr3:42577800-42578400	Enhancers	Primary T helper naive cells from peripheral blood	blood
42	chr3:42577800-42578400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
43	chr3:42577800-42578400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
44	chr3:42577800-42578400	Enhancers	Primary T helper cells PMA-I stimulated	--
45	chr3:42577800-42578800	Strong transcription	Lung	lung
46	chr3:42577800-42597600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr3:42578000-42578400	Enhancers	ES-I3 Cell Line	embryonic stem cell
48	chr3:42578000-42578400	Enhancers	Primary T cells from cord blood	blood
49	chr3:42578000-42578400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
50	chr3:42578000-42580800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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