Variant report

Variant	rs9629826
Chromosome Location	chr1:226427313-226427314
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	chr1:226422412..226424520-chr1:226427222..226429962,2	MCF-7	breast:
2	chr1:226425638..226428539-chr1:226439636..226442064,2	K562	blood:

Extended variants
information (count: 26 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10753418	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]
rs10799340	0.82[CHB][hapmap];0.87[MEX][hapmap]
rs12136759	0.87[MEX][hapmap]
rs1219652	0.85[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.83[YRI][hapmap];0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs1219654	0.87[ASN][1000 genomes]
rs1219659	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1228409	0.83[ASN][1000 genomes]
rs1361559	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs2199501	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2306119	1.00[CEU][hapmap];0.83[CHB][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2927339	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3008189	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3008190	0.96[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3008191	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3008192	0.88[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.95[MEX][hapmap];0.95[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6668540	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6703375	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7367845	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7368170	0.95[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9286999	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap]
rs9728663	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9728665	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs9629826	ACBD3	cis	normal skin	skin_eQTL
rs9629826	PARP1	cis	cerebellum	SCAN
rs9629826	ACBD3	Cis_1M	lymphoblastoid	RTeQTL
rs9629826	JMJD4	cis	parietal	SCAN

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:226412000-226427600	Weak transcription	Spleen	Spleen
2	chr1:226412000-226428000	Weak transcription	Pancreas	Pancrea
3	chr1:226412000-226429400	Weak transcription	Gastric	stomach
4	chr1:226412000-226431200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr1:226412000-226449600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr1:226412000-226455400	Weak transcription	Ovary	ovary
7	chr1:226412000-226456200	Weak transcription	NH-A	brain
8	chr1:226412000-226460600	Weak transcription	Aorta	Aorta
9	chr1:226412200-226428000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr1:226412200-226437200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr1:226412200-226448000	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr1:226412200-226456200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr1:226412200-226485400	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr1:226412400-226435600	Weak transcription	Hela-S3	cervix
15	chr1:226412400-226442600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr1:226412400-226443000	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr1:226412400-226443000	Weak transcription	Osteobl	bone
18	chr1:226412400-226446800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr1:226413000-226445000	Weak transcription	Fetal Muscle Trunk	muscle
20	chr1:226413000-226448600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr1:226413200-226456200	Weak transcription	NHDF-Ad	bronchial
22	chr1:226413600-226429200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
23	chr1:226413600-226440600	Weak transcription	Thymus	Thymus
24	chr1:226413600-226447000	Weak transcription	Brain Germinal Matrix	brain
25	chr1:226413600-226447800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr1:226414000-226428600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr1:226414000-226436600	Weak transcription	Fetal Muscle Leg	muscle
28	chr1:226414000-226456800	Weak transcription	Fetal Kidney	kidney
29	chr1:226414200-226447200	Weak transcription	Primary T cells fromperipheralblood	blood
30	chr1:226414200-226454400	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr1:226414600-226457000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr1:226414800-226443000	Weak transcription	Placenta	Placenta
33	chr1:226414800-226484600	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr1:226415400-226473800	Weak transcription	Rectal Mucosa Donor 29	rectum
35	chr1:226415600-226450000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
36	chr1:226415800-226495400	Weak transcription	Liver	Liver
37	chr1:226416200-226430000	Strong transcription	Dnd41	blood
38	chr1:226416200-226495600	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr1:226416400-226457400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
40	chr1:226416800-226443400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr1:226417000-226429000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr1:226417000-226438000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr1:226417400-226432200	Weak transcription	Fetal Heart	heart
44	chr1:226417400-226440400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr1:226417800-226428800	Strong transcription	HUES64 Cell Line	embryonic stem cell
46	chr1:226418200-226432400	Weak transcription	Fetal Intestine Large	intestine
47	chr1:226418200-226437200	Weak transcription	Left Ventricle	heart
48	chr1:226418400-226455400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
49	chr1:226418400-226484600	Weak transcription	Right Ventricle	heart
50	chr1:226418800-226435400	Weak transcription	HUVEC	blood vessel

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