Variant report

Variant	rs10753418
Chromosome Location	chr1:226473296-226473297
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:226249763..226251316-chr1:226473149..226474908,2	MCF-7	breast:
2	chr1:226464969..226471191-chr1:226471370..226476817,8	K562	blood:
3	chr1:226458655..226460444-chr1:226472837..226474997,2	K562	blood:
4	chr1:226466295..226469274-chr1:226471370..226476261,5	K562	blood:

Variant related genes	Relation type
ENSG00000163041	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10799340	0.87[MEX][hapmap]
rs10915971	0.80[CHB][hapmap]
rs12136759	0.87[MEX][hapmap]
rs1219652	0.84[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];0.83[YRI][hapmap]
rs1219659	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.80[EUR][1000 genomes]
rs1361559	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2199501	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2306119	1.00[CEU][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap]
rs3008190	0.96[CEU][hapmap];0.89[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap]
rs3008192	0.88[ASW][hapmap];0.96[CEU][hapmap];0.85[CHB][hapmap];0.90[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.93[LWK][hapmap];0.95[MEX][hapmap];0.95[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap]
rs6668540	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6703375	0.84[EUR][1000 genomes]
rs7367845	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7368170	0.95[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9286999	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9629826	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832759	chr1:226303760-226504170	Weak transcription Genic enhancers Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats 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	42 gene(s)	inside rSNPs	diseases
2	esv2829936	chr1:226375267-226488826	Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
3	nsv517107	chr1:226375267-226508645	Transcr. at gene 5' and 3' Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv873233	chr1:226385623-226508645	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	esv1825303	chr1:226458998-226481551	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	nsv832770	chr1:226465130-226655512	Strong transcription Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10753418	CDC42BPA	cis	lymphoblastoid	seeQTL
rs10753418	ACBD3	Cis_1M	lymphoblastoid	RTeQTL
rs10753418	JMJD4	cis	parietal	SCAN
rs10753418	PARP1	cis	cerebellum	SCAN

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:226412200-226485400	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr1:226414800-226484600	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr1:226415400-226473800	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr1:226415800-226495400	Weak transcription	Liver	Liver
5	chr1:226416200-226495600	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr1:226418400-226484600	Weak transcription	Right Ventricle	heart
7	chr1:226425000-226474200	Weak transcription	Primary T helper cells PMA-I stimulated	--
8	chr1:226434200-226496000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr1:226436800-226496000	Weak transcription	Esophagus	oesophagus
10	chr1:226438400-226473400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr1:226448200-226492800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr1:226448200-226495600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr1:226449800-226484000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr1:226450000-226484400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr1:226450800-226495600	Weak transcription	Adipose Nuclei	Adipose
16	chr1:226451000-226483400	Weak transcription	Duodenum Mucosa	Duodenum
17	chr1:226451200-226474600	Weak transcription	Primary B cells from cord blood	blood
18	chr1:226451200-226481000	Weak transcription	Fetal Brain Female	brain
19	chr1:226451200-226489000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr1:226451800-226474000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr1:226451800-226474000	Weak transcription	HUVEC	blood vessel
22	chr1:226451800-226480000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr1:226452000-226481800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr1:226452000-226496000	Weak transcription	Fetal Lung	lung
25	chr1:226452800-226482400	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr1:226453400-226478200	Weak transcription	Fetal Intestine Large	intestine
27	chr1:226453400-226484600	Weak transcription	Primary T cells fromperipheralblood	blood
28	chr1:226453600-226473800	Weak transcription	Primary T helper cells fromperipheralblood	blood
29	chr1:226455000-226486000	Weak transcription	Spleen	Spleen
30	chr1:226456600-226483800	Weak transcription	Ovary	ovary
31	chr1:226456600-226484000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr1:226456600-226496000	Weak transcription	Brain Angular Gyrus	brain
33	chr1:226456800-226483200	Weak transcription	Primary T cells from cord blood	blood
34	chr1:226457000-226495600	Weak transcription	Fetal Kidney	kidney
35	chr1:226457200-226474200	Weak transcription	Osteobl	bone
36	chr1:226457200-226483600	Weak transcription	GM12878-XiMat	blood
37	chr1:226457200-226495600	Weak transcription	NHDF-Ad	bronchial
38	chr1:226457200-226495600	Weak transcription	NHLF	lung
39	chr1:226457400-226477000	Weak transcription	HepG2	liver
40	chr1:226457400-226483200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
41	chr1:226457400-226495800	Weak transcription	Brain Anterior Caudate	brain
42	chr1:226457600-226474600	Weak transcription	HMEC	breast
43	chr1:226460800-226473800	Weak transcription	HSMM	muscle
44	chr1:226460800-226474200	Weak transcription	Left Ventricle	heart
45	chr1:226460800-226474400	Weak transcription	Fetal Muscle Leg	muscle
46	chr1:226460800-226496000	Weak transcription	Gastric	stomach
47	chr1:226460800-226496000	Weak transcription	Pancreas	Pancrea
48	chr1:226461000-226485800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr1:226461200-226481400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr1:226461200-226496200	Weak transcription	Aorta	Aorta

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