Variant report

Variant	rs9997920
Chromosome Location	chr4:48842672-48842673
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:48832329..48839135-chr4:48842644..48848925,12	K562	blood:
2	chr4:48841418..48843330-chr4:48847945..48850316,3	K562	blood:

Variant related genes	Relation type
ENSG00000109180	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10049761	0.91[CHB][hapmap];0.83[TSI][hapmap];0.81[YRI][hapmap]
rs10517231	0.81[ASN][1000 genomes]
rs10938537	0.89[CHB][hapmap]
rs11727343	1.00[ASW][hapmap];0.81[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11729065	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11733534	1.00[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.98[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];0.93[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11734191	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11737677	0.86[CHB][hapmap];0.85[MEX][hapmap];0.85[YRI][hapmap]
rs12374247	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12504699	0.91[JPT][hapmap]
rs12512637	0.82[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12641022	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13109500	0.80[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs13119041	0.86[CHB][hapmap];0.83[LWK][hapmap];0.85[MEX][hapmap];0.82[MKK][hapmap];0.93[YRI][hapmap]
rs13141838	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13142540	0.85[CEU][hapmap];0.91[CHB][hapmap];0.89[YRI][hapmap];0.83[EUR][1000 genomes]
rs13149083	0.88[ASW][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.93[LWK][hapmap];0.95[MEX][hapmap];0.99[MKK][hapmap];0.80[TSI][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs13152270	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1455940	0.80[ASN][1000 genomes]
rs1517674	0.91[CHB][hapmap];0.81[ASN][1000 genomes]
rs1554256	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]
rs1589107	0.80[EUR][1000 genomes]
rs2056201	0.81[ASN][1000 genomes]
rs2085292	0.81[CEU][hapmap];0.83[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.81[LWK][hapmap];0.89[MEX][hapmap];1.00[YRI][hapmap];0.80[ASN][1000 genomes]
rs2102397	0.86[CHB][hapmap];0.81[MEX][hapmap]
rs2176460	0.82[CHB][hapmap]
rs2247481	0.82[ASW][hapmap];0.87[LWK][hapmap];0.85[YRI][hapmap]
rs2289065	0.81[CHD][hapmap];0.85[JPT][hapmap]
rs2290516	0.82[CHB][hapmap];0.93[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.83[LWK][hapmap];1.00[YRI][hapmap]
rs2572345	0.82[CHB][hapmap];0.89[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.87[TSI][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2572350	0.86[CHB][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap];0.84[TSI][hapmap];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2605267	0.82[JPT][hapmap];0.84[MEX][hapmap]
rs2712156	0.86[CHB][hapmap];0.87[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.87[TSI][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2712157	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2712158	0.89[CHD][hapmap];0.93[GIH][hapmap];0.82[JPT][hapmap];0.84[TSI][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2712159	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2883562	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34730980	0.85[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs3761729	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4694904	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4694906	0.87[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4695407	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];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6447666	0.88[CEU][hapmap];0.95[GIH][hapmap];0.95[TSI][hapmap];0.83[EUR][1000 genomes]
rs6447670	0.85[AFR][1000 genomes]
rs6825639	0.82[AMR][1000 genomes]
rs724598	0.80[ASN][1000 genomes]
rs7654032	0.95[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs7657332	0.82[CHB][hapmap]
rs7657698	0.82[CHB][hapmap]
rs7660206	0.95[CHB][hapmap];0.85[MEX][hapmap];0.85[YRI][hapmap];0.80[EUR][1000 genomes]
rs7665209	0.82[CHB][hapmap];0.87[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.84[TSI][hapmap];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7667288	0.86[CHB][hapmap];0.85[MEX][hapmap];0.85[YRI][hapmap]
rs7687992	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7697522	0.82[CHB][hapmap]
rs9291326	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9637562	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]

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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9997920	OCIAD2	cis	lymphoblastoid	seeQTL
rs9997920	OCIAD2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:48834000-48859800	Weak transcription	Aorta	Aorta
2	chr4:48834000-48864600	Weak transcription	Stomach Mucosa	stomach
3	chr4:48834200-48847600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr4:48834800-48856600	Strong transcription	Primary monocytes fromperipheralblood	blood
5	chr4:48835000-48846000	Weak transcription	Right Atrium	heart
6	chr4:48835000-48848600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
7	chr4:48835000-48858000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr4:48835000-48859800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr4:48835000-48861400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr4:48835000-48862400	Strong transcription	Fetal Thymus	thymus
11	chr4:48835000-48863000	Strong transcription	HUES6 Cell Line	embryonic stem cell
12	chr4:48835000-48864400	Strong transcription	HSMM	muscle
13	chr4:48835200-48848600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr4:48835200-48863200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
15	chr4:48835200-48863800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr4:48835200-48864200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr4:48835400-48842800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr4:48835400-48843800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr4:48835400-48844800	Weak transcription	Fetal Brain Male	brain
20	chr4:48835400-48850400	Strong transcription	K562	blood
21	chr4:48835400-48857400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr4:48835400-48863200	Strong transcription	Monocytes-CD14+_RO01746	blood
23	chr4:48835400-48863400	Strong transcription	HUES48 Cell Line	embryonic stem cell
24	chr4:48835600-48845400	Strong transcription	Osteobl	bone
25	chr4:48835600-48847400	Weak transcription	Fetal Heart	heart
26	chr4:48835600-48848600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr4:48835600-48856200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr4:48835600-48864000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr4:48835800-48843000	Strong transcription	Fetal Intestine Large	intestine
30	chr4:48835800-48845800	Strong transcription	Fetal Lung	lung
31	chr4:48835800-48848200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
32	chr4:48835800-48848400	Strong transcription	Rectal Mucosa Donor 29	rectum
33	chr4:48835800-48856200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
34	chr4:48835800-48857000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr4:48835800-48857000	Strong transcription	Primary T helper cells fromperipheralblood	blood
36	chr4:48835800-48863200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr4:48836000-48844600	Weak transcription	Hela-S3	cervix
38	chr4:48836000-48849600	Strong transcription	Placenta	Placenta
39	chr4:48836000-48858000	Weak transcription	Pancreatic Islets	Pancreatic Islet
40	chr4:48836000-48863600	Strong transcription	HUES64 Cell Line	embryonic stem cell
41	chr4:48836200-48848800	Strong transcription	Cortex derived primary cultured neurospheres	brain
42	chr4:48836200-48854800	Strong transcription	Primary B cells from cord blood	blood
43	chr4:48836200-48863600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
44	chr4:48836400-48843800	Strong transcription	Fetal Muscle Trunk	muscle
45	chr4:48836400-48848200	Strong transcription	Rectal Mucosa Donor 31	rectum
46	chr4:48836400-48850400	Strong transcription	Primary T cells fromperipheralblood	blood
47	chr4:48836400-48850400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr4:48836400-48857200	Strong transcription	Primary B cells from peripheral blood	blood
49	chr4:48836600-48843400	Strong transcription	Primary neutrophils fromperipheralblood	blood
50	chr4:48836600-48843800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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