Variant report

Variant	rs1396117
Chromosome Location	chr8:57871922-57871923
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:57869598..57872187-chr8:57872498..57874504,2	K562	blood:
2	chr8:57871386..57873031-chr8:57904791..57907471,2	MCF-7	breast:
3	chr8:57844913..57847717-chr8:57870990..57872662,2	MCF-7	breast:
4	chr8:57871408..57873371-chr8:57876087..57877926,2	K562	blood:

Variant related genes	Relation type
ENSG00000104331	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10003	0.83[CEU][hapmap]
rs1044731	0.83[CEU][hapmap]
rs10504211	1.00[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10504212	1.00[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10808910	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10958514	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10958515	1.00[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11778484	1.00[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11779511	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12056416	0.84[CEU][hapmap]
rs12678538	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13258916	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13275472	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13277865	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1396115	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1396116	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1605556	1.00[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16921462	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16921483	0.84[CEU][hapmap];0.88[YRI][hapmap];0.84[AFR][1000 genomes]
rs16921485	0.84[AFR][1000 genomes]
rs2135987	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34020186	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs36065736	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4738558	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55659168	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs967930	1.00[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1029443	chr8:57748114-58057656	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	esv3430321	chr8:57858417-58055129	Strong transcription Genic enhancers Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1396117	IMPAD1	cis	multi-tissue	Pritchard

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:57863400-57874800	Weak transcription	Colon Smooth Muscle	Colon
2	chr8:57863800-57878200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr8:57866400-57876200	Weak transcription	Rectal Smooth Muscle	rectum
4	chr8:57866400-57878600	Weak transcription	Ovary	ovary
5	chr8:57866400-57902600	Weak transcription	Pancreas	Pancrea
6	chr8:57866600-57872800	Weak transcription	Right Ventricle	heart
7	chr8:57866600-57874800	Weak transcription	Placenta	Placenta
8	chr8:57866600-57875400	Weak transcription	Fetal Lung	lung
9	chr8:57866600-57876000	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr8:57866600-57876400	Weak transcription	Brain Hippocampus Middle	brain
11	chr8:57866800-57872600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr8:57866800-57872600	Weak transcription	Adipose Nuclei	Adipose
13	chr8:57866800-57873200	Weak transcription	Primary T helper cells fromperipheralblood	blood
14	chr8:57866800-57873200	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr8:57866800-57874600	Weak transcription	HSMM	muscle
16	chr8:57866800-57875200	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr8:57866800-57876000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr8:57866800-57876200	Weak transcription	Left Ventricle	heart
19	chr8:57866800-57880800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr8:57866800-57890000	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr8:57867000-57873400	Weak transcription	Primary T cells from cord blood	blood
22	chr8:57867000-57876200	Weak transcription	Brain Germinal Matrix	brain
23	chr8:57867000-57876200	Weak transcription	Thymus	Thymus
24	chr8:57867600-57875600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr8:57867600-57881400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr8:57867800-57872600	Weak transcription	Fetal Intestine Large	intestine
27	chr8:57867800-57874600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr8:57868000-57872800	Weak transcription	Primary T helper cells PMA-I stimulated	--
29	chr8:57868000-57875400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr8:57868200-57872800	Weak transcription	Liver	Liver
31	chr8:57868400-57872800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr8:57868400-57876200	Weak transcription	Psoas Muscle	Psoas
33	chr8:57868400-57878600	Weak transcription	Aorta	Aorta
34	chr8:57868600-57875000	Weak transcription	HUES64 Cell Line	embryonic stem cell
35	chr8:57868600-57876200	Weak transcription	Brain Cingulate Gyrus	brain
36	chr8:57868600-57878400	Weak transcription	Fetal Brain Female	brain
37	chr8:57868800-57872600	Weak transcription	Primary T cells fromperipheralblood	blood
38	chr8:57868800-57876200	Weak transcription	Fetal Intestine Small	intestine
39	chr8:57868800-57876200	Weak transcription	Fetal Muscle Trunk	muscle
40	chr8:57868800-57878400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr8:57868800-57895800	Weak transcription	Spleen	Spleen
42	chr8:57869000-57873400	Weak transcription	Rectal Mucosa Donor 29	rectum
43	chr8:57869000-57874800	Weak transcription	GM12878-XiMat	blood
44	chr8:57869000-57896000	Weak transcription	Esophagus	oesophagus
45	chr8:57869400-57874600	Weak transcription	Fetal Thymus	thymus
46	chr8:57869400-57875000	Weak transcription	Hela-S3	cervix
47	chr8:57869400-57875400	Weak transcription	NHDF-Ad	bronchial
48	chr8:57869400-57881800	Weak transcription	Stomach Mucosa	stomach
49	chr8:57869600-57875400	Weak transcription	Fetal Kidney	kidney
50	chr8:57869800-57874400	Weak transcription	Primary hematopoietic stem cells short term culture	blood

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