Variant report

Variant	rs4695397
Chromosome Location	chr4:48712506-48712507
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 103 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs10003273	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10008265	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10049761	0.95[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.83[EUR][1000 genomes]
rs10938534	0.93[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap]
rs10938537	0.95[JPT][hapmap]
rs11727343	0.82[CEU][hapmap]
rs11737677	0.95[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap]
rs11939889	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11943219	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12512637	0.92[CEU][hapmap];0.91[CHB][hapmap];1.00[YRI][hapmap]
rs13113370	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13119041	0.95[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap]
rs13119414	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13119504	0.82[EUR][1000 genomes]
rs13141838	0.81[EUR][1000 genomes]
rs13142540	0.83[CHB][hapmap];1.00[JPT][hapmap]
rs1507865	1.00[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs1517674	0.82[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs1554256	0.82[CHB][hapmap];0.81[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1554258	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1589107	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs16861510	0.83[YRI][hapmap]
rs1702798	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1712767	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1712772	0.82[CEU][hapmap];0.93[YRI][hapmap];0.84[EUR][1000 genomes]
rs17575720	1.00[JPT][hapmap]
rs17656040	0.91[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs17656094	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs1876469	0.95[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap]
rs1980193	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2056201	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2102397	0.93[GIH][hapmap];0.91[JPT][hapmap];0.85[TSI][hapmap];0.92[YRI][hapmap]
rs2176460	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2289065	1.00[YRI][hapmap]
rs2354314	0.84[AFR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2354348	0.93[GIH][hapmap];0.95[JPT][hapmap];0.80[MKK][hapmap];0.84[TSI][hapmap]
rs2354938	0.96[MKK][hapmap];1.00[YRI][hapmap]
rs2572345	0.83[ASW][hapmap];0.92[CEU][hapmap];0.91[CHB][hapmap];0.83[MKK][hapmap];1.00[YRI][hapmap]
rs2572350	0.91[ASW][hapmap];0.85[CEU][hapmap];0.81[CHB][hapmap];0.81[MKK][hapmap]
rs2712156	0.83[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];0.83[MKK][hapmap];1.00[YRI][hapmap]
rs2712158	0.83[ASW][hapmap];0.92[CEU][hapmap];0.86[CHB][hapmap];0.84[MKK][hapmap];1.00[YRI][hapmap]
rs28470767	0.95[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap]
rs28733443	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2940324	0.85[EUR][1000 genomes]
rs3107022	0.82[EUR][1000 genomes]
rs4536901	1.00[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap]
rs4694906	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[YRI][hapmap]
rs4695391	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs4695400	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4695401	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4695407	0.81[CHB][hapmap]
rs57797824	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62309747	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6447651	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6447655	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6447660	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6811148	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs6814811	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6830078	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6830848	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6843340	0.93[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap]
rs6853588	0.80[EUR][1000 genomes]
rs7657332	0.92[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7657698	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7660206	0.87[CHB][hapmap];0.81[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7665209	0.92[CEU][hapmap];0.91[CHB][hapmap];0.81[GIH][hapmap]
rs7667288	0.95[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap]
rs7670939	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7679210	1.00[JPT][hapmap]
rs7680280	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7681070	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7682859	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7683398	1.00[JPT][hapmap]
rs7693461	1.00[JPT][hapmap]
rs7697522	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs776584	0.93[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[EUR][1000 genomes]
rs776588	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs776591	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs776601	0.80[EUR][1000 genomes]
rs776602	0.85[YRI][hapmap]
rs796555	1.00[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[EUR][1000 genomes]
rs9291326	0.82[CHB][hapmap]
rs937888	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs937889	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.84[EUR][1000 genomes]
rs952289	1.00[JPT][hapmap]
rs955683	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9790336	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9997920	0.82[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:15 , 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	nsv999203	chr4:48645887-48735512	Enhancers Weak transcription Flanking Active TSS Strong transcription 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	esv1802666	chr4:48646594-48721327	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	nsv1013914	chr4:48652784-48728934	Genic enhancers Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
10	nsv537090	chr4:48652784-48728934	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription 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
11	esv1796692	chr4:48686817-48726266	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
12	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
13	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
14	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
15	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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4695397	OCIAD2	cis	lymphoblastoid	seeQTL
rs4695397	OCIAD1	Cis_1M	lymphoblastoid	RTeQTL
rs4695397	SLC10A4	cis	lung	GTEx
rs4695397	OCIAD2	cis	cerebellum	SCAN

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:48621200-48729400	Weak transcription	Thymus	Thymus
2	chr4:48700200-48730800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr4:48700400-48713200	Weak transcription	Placenta	Placenta
4	chr4:48700400-48718800	Weak transcription	Fetal Muscle Leg	muscle
5	chr4:48700600-48719600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr4:48700800-48715600	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr4:48701000-48713000	Weak transcription	Fetal Brain Male	brain
8	chr4:48701000-48715200	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr4:48701000-48729600	Weak transcription	Aorta	Aorta
10	chr4:48701400-48713600	Weak transcription	Fetal Brain Female	brain
11	chr4:48701800-48715400	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr4:48701800-48715800	Weak transcription	Fetal Kidney	kidney
13	chr4:48701800-48724600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr4:48702200-48716200	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr4:48702600-48717400	Weak transcription	Colon Smooth Muscle	Colon
16	chr4:48702800-48720800	Weak transcription	Small Intestine	intestine
17	chr4:48703400-48714800	Weak transcription	NH-A	brain
18	chr4:48703400-48722800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
19	chr4:48703800-48712600	Weak transcription	Osteobl	bone
20	chr4:48704000-48712600	Weak transcription	Fetal Stomach	stomach
21	chr4:48705600-48712800	Weak transcription	Psoas Muscle	Psoas
22	chr4:48705600-48728800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr4:48705800-48714000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr4:48706600-48712800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr4:48706600-48718600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
26	chr4:48707400-48720800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr4:48708400-48713000	Strong transcription	Primary B cells from peripheral blood	blood
28	chr4:48708400-48713000	Strong transcription	Primary T cells from cord blood	blood
29	chr4:48709000-48712600	Weak transcription	HMEC	breast
30	chr4:48709000-48715800	Weak transcription	Brain Hippocampus Middle	brain
31	chr4:48709000-48720200	Weak transcription	HepG2	liver
32	chr4:48709000-48723600	Weak transcription	Left Ventricle	heart
33	chr4:48709000-48724600	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr4:48709000-48726400	Weak transcription	Ovary	ovary
35	chr4:48709400-48713800	Weak transcription	Stomach Smooth Muscle	stomach
36	chr4:48709800-48714200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr4:48710200-48712600	Strong transcription	Primary monocytes fromperipheralblood	blood
38	chr4:48710200-48713000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
39	chr4:48710400-48712600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
40	chr4:48710400-48712600	Strong transcription	Primary T helper cells fromperipheralblood	blood
41	chr4:48710400-48712800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr4:48710400-48712800	Strong transcription	Fetal Thymus	thymus
43	chr4:48710400-48712800	Strong transcription	Rectal Mucosa Donor 29	rectum
44	chr4:48710400-48713000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr4:48710400-48713000	Strong transcription	Primary B cells from cord blood	blood
46	chr4:48710400-48713000	Strong transcription	Cortex derived primary cultured neurospheres	brain
47	chr4:48710400-48713000	Strong transcription	Dnd41	blood
48	chr4:48710400-48713200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr4:48710600-48712600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr4:48710600-48712600	Strong transcription	HUES64 Cell Line	embryonic stem cell

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