Variant report

Variant	rs10008975
Chromosome Location	chr4:15624571-15624572
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	chr4:15607476..15609952-chr4:15624488..15626808,2	K562	blood:

Extended variants
information (count: 62 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10008376	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10214	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10939621	0.85[JPT][hapmap]
rs11728084	0.88[EUR][1000 genomes]
rs12499412	0.94[AFR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12500587	1.00[CEU][hapmap];0.86[MEX][hapmap];0.86[TSI][hapmap];0.90[EUR][1000 genomes]
rs12500770	0.95[AFR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12512883	0.86[EUR][1000 genomes]
rs12644655	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12649803	0.86[JPT][hapmap];0.82[MKK][hapmap]
rs12651550	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13110674	0.92[EUR][1000 genomes]
rs13120905	0.94[AFR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13129739	0.86[EUR][1000 genomes]
rs13147590	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1789	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35414597	0.87[EUR][1000 genomes]
rs4235379	0.96[CEU][hapmap];0.91[TSI][hapmap];0.92[EUR][1000 genomes]
rs4270584	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4333182	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs4453929	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4470622	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4524378	0.91[EUR][1000 genomes]
rs4557256	0.85[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.99[MKK][hapmap];0.93[TSI][hapmap];0.88[YRI][hapmap];0.97[AFR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4616746	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4631041	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4698402	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4698404	0.89[AFR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4698406	0.92[EUR][1000 genomes]
rs4698407	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4698409	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61021642	0.90[EUR][1000 genomes]
rs6414765	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6414767	0.97[AFR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6414768	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6449146	0.86[JPT][hapmap];0.83[MKK][hapmap]
rs6449147	0.86[JPT][hapmap]
rs6449153	0.95[EUR][1000 genomes]
rs6449161	1.00[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.86[MEX][hapmap];0.92[MKK][hapmap];0.80[TSI][hapmap];0.85[YRI][hapmap];0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6850169	0.83[EUR][1000 genomes]
rs6850422	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.86[TSI][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7438356	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];0.92[YRI][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs759212	0.86[JPT][hapmap]
rs7662032	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7685083	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7687003	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7688984	0.94[EUR][1000 genomes]
rs7696127	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7697314	0.86[JPT][hapmap]
rs8180240	0.81[AFR][1000 genomes]
rs9996452	0.86[JPT][hapmap]
rs9997068	0.96[AFR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3448986	chr4:14928802-15805558	Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	esv2757923	chr4:15444617-15749520	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	esv2759227	chr4:15444617-15749520	Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv428439	chr4:15556961-15749520	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
5	nsv1012988	chr4:15597510-16091527	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
6	nsv518830	chr4:15610771-15672200	Flanking Active TSS Enhancers Bivalent/Poised TSS ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	nsv521183	chr4:15610771-15692136	Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
8	esv3376437	chr4:15613963-15626944	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
9	esv3464784	chr4:15613969-15626901	Strong transcription ZNF genes & repeats Weak transcription Enhancers Genic enhancers Flanking Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
10	esv3464785	chr4:15613969-15626901	ZNF genes & repeats Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10008975	FAM200B	cis	parietal	SCAN
rs10008975	FBXL5	Cis_1M	lymphoblastoid	RTeQTL
rs10008975	CC2D2A	cis	parietal	SCAN

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:15568400-15655600	Weak transcription	Gastric	stomach
2	chr4:15590600-15626400	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr4:15600800-15653000	Weak transcription	Colonic Mucosa	Colon
4	chr4:15601000-15651600	Weak transcription	Small Intestine	intestine
5	chr4:15602000-15626000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr4:15602600-15655600	Weak transcription	Pancreas	Pancrea
7	chr4:15603800-15626800	Weak transcription	NHLF	lung
8	chr4:15605400-15625800	Weak transcription	HMEC	breast
9	chr4:15605800-15650200	Weak transcription	Stomach Mucosa	stomach
10	chr4:15606000-15633800	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr4:15612800-15625200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr4:15613400-15625800	Weak transcription	NH-A	brain
13	chr4:15613400-15626200	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr4:15613400-15635000	Weak transcription	HSMMtube	muscle
15	chr4:15613600-15626000	Weak transcription	Placenta	Placenta
16	chr4:15615600-15625000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr4:15617800-15624600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr4:15617800-15627400	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr4:15618000-15624600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr4:15618600-15625800	Weak transcription	Brain Cingulate Gyrus	brain
21	chr4:15618600-15626000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr4:15618600-15627000	Weak transcription	Right Ventricle	heart
23	chr4:15618600-15651000	Weak transcription	Spleen	Spleen
24	chr4:15620400-15624600	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
25	chr4:15620600-15624800	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
26	chr4:15620800-15626800	Weak transcription	Lung	lung
27	chr4:15621000-15624800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr4:15621000-15624800	ZNF genes & repeats	Dnd41	blood
29	chr4:15621000-15632600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr4:15621200-15624600	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
31	chr4:15621200-15625200	ZNF genes & repeats	GM12878-XiMat	blood
32	chr4:15621600-15625800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr4:15621600-15625800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr4:15621600-15625800	Weak transcription	Osteobl	bone
35	chr4:15621600-15627000	Weak transcription	Brain Angular Gyrus	brain
36	chr4:15621800-15624600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr4:15621800-15625600	Weak transcription	HUVEC	blood vessel
38	chr4:15621800-15625800	Weak transcription	Fetal Kidney	kidney
39	chr4:15621800-15625800	Weak transcription	Rectal Mucosa Donor 29	rectum
40	chr4:15621800-15626000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
41	chr4:15621800-15626000	Weak transcription	Stomach Smooth Muscle	stomach
42	chr4:15621800-15626000	Weak transcription	NHEK	skin
43	chr4:15621800-15626200	Weak transcription	Hela-S3	cervix
44	chr4:15621800-15626400	Weak transcription	Skeletal Muscle Female	skeletal muscle
45	chr4:15621800-15626800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr4:15621800-15626800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr4:15621800-15626800	Weak transcription	Rectal Smooth Muscle	rectum
48	chr4:15621800-15627000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
49	chr4:15621800-15627000	Weak transcription	Esophagus	oesophagus
50	chr4:15621800-15627000	Weak transcription	Psoas Muscle	Psoas

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