Variant report

Variant	rs2304387
Chromosome Location	chr4:48834573-48834574
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:48780694..48783941-chr4:48830567..48835952,11	MCF-7	breast:
2	chr4:48780685..48782941-chr4:48832386..48835907,3	MCF-7	breast:
3	chr4:48781848..48784199-chr4:48833719..48835866,2	K562	blood:
4	chr4:48834344..48836920-chr4:48860620..48862528,2	K562	blood:
5	chr4:48746546..48749317-chr4:48834031..48835783,2	K562	blood:

Variant related genes	Relation type
ENSG00000075539	Chromatin interaction
ENSG00000248256	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10938546	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs12509766	1.00[CHB][hapmap];1.00[GIH][hapmap];0.85[TSI][hapmap]
rs1517675	1.00[CHB][hapmap]
rs1712762	1.00[CHB][hapmap];0.85[TSI][hapmap]
rs17610725	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17656727	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17656763	1.00[CHB][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1824039	0.85[EUR][1000 genomes]
rs1824040	0.85[EUR][1000 genomes]
rs2354947	1.00[ASN][1000 genomes]
rs2354948	1.00[ASN][1000 genomes]
rs45463191	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62310925	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6447674	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs73815372	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs746513	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs776586	1.00[CHB][hapmap]
rs776593	1.00[CHB][hapmap];1.00[GIH][hapmap];0.85[TSI][hapmap]
rs776594	1.00[CHB][hapmap];1.00[GIH][hapmap];0.85[TSI][hapmap]
rs776596	1.00[CHB][hapmap];0.85[TSI][hapmap]
rs776597	1.00[CHB][hapmap];1.00[GIH][hapmap];0.85[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002674	chr4:48507608-49032909	Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv537087	chr4:48507608-49032909	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv1010923	chr4:48575156-49083089	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv537088	chr4:48575156-49083089	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	nsv1013762	chr4:48580484-49032909	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv537089	chr4:48580484-49032909	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
7	esv1793455	chr4:48686817-48859142	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv1010381	chr4:48701525-49309842	Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Weak transcription Genic enhancers Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
9	nsv1003718	chr4:48771947-49083089	Active TSS Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
10	nsv916809	chr4:48784318-49083302	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
11	nsv1011910	chr4:48784332-49154757	ZNF genes & repeats Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
12	nsv879010	chr4:48794403-49061141	Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
13	nsv1008733	chr4:48827603-48971172	Enhancers Genic enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
14	nsv427680	chr4:48829607-49660117	ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:48832200-48834800	Active TSS	Stomach Smooth Muscle	stomach
2	chr4:48832400-48834600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
3	chr4:48832400-48834600	Active TSS	NH-A	brain
4	chr4:48832400-48834800	Active TSS	Fetal Kidney	kidney
5	chr4:48832400-48835000	Active TSS	ES-I3 Cell Line	embryonic stem cell
6	chr4:48832400-48835200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr4:48832600-48834600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr4:48832600-48834600	Active TSS	Liver	Liver
9	chr4:48832600-48834600	Active TSS	Fetal Muscle Trunk	muscle
10	chr4:48832600-48834600	Active TSS	Rectal Mucosa Donor 31	rectum
11	chr4:48832600-48834600	Active TSS	HSMM	muscle
12	chr4:48832600-48834800	Active TSS	Psoas Muscle	Psoas
13	chr4:48832600-48834800	Active TSS	Right Ventricle	heart
14	chr4:48832600-48834800	Active TSS	NHLF	lung
15	chr4:48832600-48835000	Active TSS	H1 Cell Line	embryonic stem cell
16	chr4:48832600-48835000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr4:48832600-48835000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr4:48832800-48834600	Active TSS	HUES6 Cell Line	embryonic stem cell
19	chr4:48832800-48834600	Active TSS	iPS-18 Cell Line	embryonic stem cell
20	chr4:48832800-48834600	Active TSS	Brain Angular Gyrus	brain
21	chr4:48832800-48834600	Active TSS	Fetal Intestine Large	intestine
22	chr4:48832800-48834600	Active TSS	HMEC	breast
23	chr4:48832800-48834600	Active TSS	K562	blood
24	chr4:48832800-48834600	Active TSS	NHEK	skin
25	chr4:48832800-48834800	Active TSS	iPS-20b Cell Line	embryonic stem cell
26	chr4:48832800-48834800	Active TSS	A549	lung
27	chr4:48832800-48834800	Active TSS	Hela-S3	cervix
28	chr4:48832800-48834800	Active TSS	HSMMtube	muscle
29	chr4:48832800-48835200	Active TSS	iPS-15b Cell Line	embryonic stem cell
30	chr4:48832800-48835600	Active TSS	GM12878-XiMat	blood
31	chr4:48833000-48834600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr4:48833000-48834600	Active TSS	Primary hematopoietic stem cells short term culture	blood
33	chr4:48833000-48834600	Active TSS	Fetal Muscle Leg	muscle
34	chr4:48833000-48835000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr4:48833600-48834800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr4:48833600-48834800	Active TSS	Right Atrium	heart
37	chr4:48833600-48835200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr4:48833800-48834600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
39	chr4:48833800-48834800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr4:48833800-48834800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr4:48833800-48834800	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
42	chr4:48833800-48836400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr4:48833800-48836400	Weak transcription	Spleen	Spleen
44	chr4:48834000-48834600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
45	chr4:48834000-48834600	Flanking Active TSS	Duodenum Mucosa	Duodenum
46	chr4:48834000-48834600	Weak transcription	Left Ventricle	heart
47	chr4:48834000-48834600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
48	chr4:48834000-48834600	Weak transcription	Sigmoid Colon	Sigmoid Colon
49	chr4:48834000-48834600	Weak transcription	Small Intestine	intestine
50	chr4:48834000-48834600	Active TSS	HepG2	liver

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