Variant report

Variant	rs1554256
Chromosome Location	chr4:48764009-48764010
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:48763131..48767010-chr4:48780042..48783198,3	K562	blood:

Variant related genes	Relation type
ENSG00000075539	Chromatin interaction

Extended variants
information (count: 88 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs10003273	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10008265	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10010571	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10049761	0.88[ASW][hapmap];0.96[CEU][hapmap];0.86[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.85[YRI][hapmap];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10938537	0.92[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes]
rs11727343	0.96[CEU][hapmap];0.86[CHB][hapmap];0.84[CHD][hapmap];0.81[GIH][hapmap];0.87[LWK][hapmap];0.90[MEX][hapmap];0.82[MKK][hapmap];0.88[TSI][hapmap];0.96[YRI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11728565	0.83[AMR][1000 genomes]
rs11729065	0.80[EUR][1000 genomes]
rs11733534	0.81[CHB][hapmap];0.82[LWK][hapmap];0.84[MEX][hapmap];0.85[MKK][hapmap];0.89[YRI][hapmap];0.80[EUR][1000 genomes]
rs11737677	0.88[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.82[AMR][1000 genomes]
rs11939889	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11943219	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13108474	0.81[AMR][1000 genomes]
rs13108799	0.80[AMR][1000 genomes]
rs13113370	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13119041	1.00[ASW][hapmap];0.96[CEU][hapmap];0.87[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap]
rs13119414	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13119504	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13142540	0.92[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13149083	0.92[CEU][hapmap];0.86[CHB][hapmap];0.84[CHD][hapmap];0.85[LWK][hapmap];0.90[MEX][hapmap];0.84[MKK][hapmap];0.92[YRI][hapmap];0.80[AMR][1000 genomes]
rs13151534	0.82[AMR][1000 genomes]
rs1507865	0.98[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap]
rs1517674	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1554258	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1589107	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17575720	0.96[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap]
rs1876469	1.00[ASW][hapmap];0.96[CEU][hapmap];0.87[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes]
rs1980193	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2056201	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2085292	0.85[MEX][hapmap];0.96[YRI][hapmap]
rs2102397	0.96[CEU][hapmap];0.87[CHB][hapmap];0.84[CHD][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap]
rs2176460	0.82[CHB][hapmap];0.85[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2247481	0.81[YRI][hapmap]
rs2290516	0.96[YRI][hapmap]
rs2354312	0.91[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2354314	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2354348	0.96[CEU][hapmap];0.87[CHB][hapmap];0.86[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap]
rs28470767	0.88[ASW][hapmap];0.96[CEU][hapmap];0.87[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap]
rs3761729	0.81[CEU][hapmap];0.86[CHB][hapmap];0.82[LWK][hapmap];0.85[MEX][hapmap];0.84[MKK][hapmap];0.92[YRI][hapmap];0.80[EUR][1000 genomes]
rs4694904	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4695391	0.93[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap]
rs4695397	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4695400	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4695401	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4695407	0.91[CHB][hapmap];0.96[YRI][hapmap];0.80[EUR][1000 genomes]
rs57797824	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6447651	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6447655	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6447666	0.81[GIH][hapmap]
rs6814811	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6818954	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6830078	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6830848	1.00[JPT][hapmap]
rs6843340	0.96[CEU][hapmap];0.91[CHB][hapmap];0.87[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes]
rs7654032	0.92[CEU][hapmap];0.86[CHB][hapmap];0.92[YRI][hapmap];0.80[AMR][1000 genomes]
rs7657332	0.82[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7657698	0.82[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7660206	0.88[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7667288	0.88[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7670939	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7679210	0.96[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap]
rs7680280	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7681070	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7682859	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7693461	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap]
rs7697522	0.82[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs776584	1.00[JPT][hapmap]
rs776591	1.00[JPT][hapmap]
rs796555	0.95[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap]
rs9291326	0.89[ASW][hapmap];0.91[CHB][hapmap];0.85[LWK][hapmap];0.85[MEX][hapmap];0.89[MKK][hapmap];0.96[YRI][hapmap];0.80[EUR][1000 genomes]
rs937889	1.00[JPT][hapmap]
rs955683	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9637562	0.80[EUR][1000 genomes]
rs9790336	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9997920	0.91[CHB][hapmap];0.82[LWK][hapmap];0.85[MEX][hapmap];0.85[MKK][hapmap];0.96[YRI][hapmap];0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 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	esv1792683	chr4:48686817-48764009	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	esv1795181	chr4:48686817-48764009	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	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
10	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
11	esv1792281	chr4:48719424-48764009	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
12	esv1794245	chr4:48719424-48764009	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
13	esv1794757	chr4:48719424-48764009	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1554256	OCIAD2	cis	lymphoblastoid	seeQTL
rs1554256	OCIAD2	cis	cerebellum	SCAN
rs1554256	SLC10A4	cis	lung	GTEx

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:48731600-48779800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr4:48742000-48768400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr4:48742600-48768200	Weak transcription	Pancreas	Pancrea
4	chr4:48745000-48765200	Weak transcription	Primary B cells from cord blood	blood
5	chr4:48747200-48777200	Weak transcription	Fetal Intestine Small	intestine
6	chr4:48747400-48767800	Weak transcription	Fetal Intestine Large	intestine
7	chr4:48749200-48768200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr4:48751000-48768400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr4:48751600-48777200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr4:48752000-48767000	Weak transcription	Fetal Muscle Leg	muscle
11	chr4:48752400-48765200	Weak transcription	Primary T cells fromperipheralblood	blood
12	chr4:48753200-48764600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
13	chr4:48754600-48768000	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr4:48754800-48774200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr4:48755000-48767400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr4:48755000-48773600	Weak transcription	Aorta	Aorta
17	chr4:48755200-48765200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
18	chr4:48755200-48765400	Weak transcription	Primary B cells from peripheral blood	blood
19	chr4:48755200-48768400	Weak transcription	Fetal Thymus	thymus
20	chr4:48755200-48769400	Weak transcription	Monocytes-CD14+_RO01746	blood
21	chr4:48755200-48774200	Weak transcription	Primary neutrophils fromperipheralblood	blood
22	chr4:48755400-48768200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr4:48755400-48775600	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr4:48755600-48774800	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr4:48756000-48764200	Weak transcription	Primary T helper cells fromperipheralblood	blood
26	chr4:48756000-48773000	Weak transcription	HUVEC	blood vessel
27	chr4:48756000-48774800	Weak transcription	Primary hematopoietic stem cells	blood
28	chr4:48756200-48764400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
29	chr4:48756200-48774200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr4:48756600-48768600	Weak transcription	HUES64 Cell Line	embryonic stem cell
31	chr4:48756600-48769600	Weak transcription	Primary T cells from cord blood	blood
32	chr4:48759000-48765200	Weak transcription	Lung	lung
33	chr4:48759000-48768200	Weak transcription	Brain Substantia Nigra	brain
34	chr4:48759000-48775600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr4:48759000-48778600	Weak transcription	Fetal Stomach	stomach
36	chr4:48759200-48764200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr4:48759200-48768200	Weak transcription	Small Intestine	intestine
38	chr4:48759200-48769200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr4:48759200-48769600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr4:48759200-48775400	Weak transcription	NHEK	skin
41	chr4:48759200-48775600	Weak transcription	HMEC	breast
42	chr4:48761000-48779800	Weak transcription	Placenta	Placenta
43	chr4:48761200-48768200	Weak transcription	Esophagus	oesophagus
44	chr4:48761600-48768400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr4:48761600-48768400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr4:48761800-48767200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr4:48761800-48768400	Weak transcription	Duodenum Mucosa	Duodenum
48	chr4:48761800-48769200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
49	chr4:48762000-48764400	Weak transcription	Cortex derived primary cultured neurospheres	brain
50	chr4:48762000-48766000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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