Variant report

Variant	rs4235481
Chromosome Location	chr5:60093387-60093388
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	chr5:60091814..60093851-chr5:60098024..60100657,2	K562	blood:
2	chr5:60089577..60091620-chr5:60092032..60093773,2	K562	blood:

Extended variants
information (count: 55 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10057395	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10062839	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs10072745	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10076679	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10077663	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13158665	0.82[EUR][1000 genomes]
rs13184554	0.96[ASN][1000 genomes]
rs1445292	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs1445293	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1870015	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35006499	0.82[ASN][1000 genomes]
rs36111624	0.93[ASN][1000 genomes]
rs3936423	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4235482	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4482855	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4647078	0.84[CHD][hapmap]
rs4700392	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs4700393	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4700394	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs55809585	0.87[ASN][1000 genomes]
rs6449500	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6449501	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6449502	1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs6449503	0.93[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.96[MEX][hapmap];0.90[MKK][hapmap];0.98[TSI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6449504	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs6449505	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs6869332	0.88[CHD][hapmap];1.00[JPT][hapmap]
rs6871557	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6872863	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6873181	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6875456	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6876335	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6876346	0.91[ASN][1000 genomes]
rs6877757	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs6877849	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs6890201	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6893642	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6894672	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6894750	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7709422	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7709444	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7712473	1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs7730827	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs921897	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv492277	chr5:59905195-60180834	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
2	nsv462198	chr5:59969015-60116613	Strong transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv598298	chr5:59969015-60116613	ZNF genes & repeats Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv934153	chr5:60004982-60309751	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
5	esv2763456	chr5:60007355-60151767	Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
6	nsv1026190	chr5:60020156-60148535	Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
7	nsv537769	chr5:60020156-60148535	Weak transcription Bivalent Enhancer Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
8	esv2752073	chr5:60034475-60136626	Weak transcription Strong transcription Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	diseases
9	nsv949662	chr5:60047974-60488379	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
10	nsv1017095	chr5:60050600-60414783	Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
11	nsv933326	chr5:60074031-60413061	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4235481	ERCC8	cis	lymphoblastoid	seeQTL
rs4235481	ERCC8	Cis_1M	lymphoblastoid	RTeQTL
rs4235481	DEPDC1B	cis	cerebellum	SCAN

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:60044800-60098000	Weak transcription	Primary hematopoietic stem cells	blood
2	chr5:60065200-60101200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr5:60080200-60101400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr5:60082400-60112600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr5:60090800-60097400	Weak transcription	Duodenum Mucosa	Duodenum
6	chr5:60091000-60093400	Weak transcription	Fetal Intestine Large	intestine
7	chr5:60091000-60096400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr5:60091200-60104200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr5:60091400-60105200	Weak transcription	K562	blood
10	chr5:60092200-60093600	Enhancers	Brain Anterior Caudate	brain
11	chr5:60092400-60096400	Weak transcription	Fetal Intestine Small	intestine
12	chr5:60092800-60094000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
13	chr5:60092800-60110400	Weak transcription	Brain Substantia Nigra	brain
14	chr5:60093000-60093400	Enhancers	H1 Cell Line	embryonic stem cell
15	chr5:60093000-60093400	Enhancers	iPS-18 Cell Line	embryonic stem cell
16	chr5:60093000-60093600	Enhancers	Brain Cingulate Gyrus	brain
17	chr5:60093000-60093600	Enhancers	Brain Hippocampus Middle	brain
18	chr5:60093200-60093600	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
19	chr5:60093200-60093600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr5:60093200-60093600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr5:60093200-60093600	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
22	chr5:60093200-60093600	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
23	chr5:60093200-60093600	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
24	chr5:60093200-60093600	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
25	chr5:60093200-60093600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr5:60093200-60093800	Enhancers	Pancreas	Pancrea
27	chr5:60093200-60094200	Enhancers	H9 Cell Line	embryonic stem cell
28	chr5:60093200-60094200	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
29	chr5:60093200-60094200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell

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