Variant report

Variant	rs10254398
Chromosome Location	chr7:7686514-7686515
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:7685666..7688418-chr7:7688824..7691434,2	K562	blood:
2	chr7:7680700..7683473-chr7:7685626..7688056,2	MCF-7	breast:
3	chr7:7676999..7684981-chr7:7684990..7693882,16	K562	blood:

Variant related genes	Relation type
ENSG00000106399	Chromatin interaction
ENSG00000219545	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs10230651	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10234456	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10235747	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10253697	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12538804	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.87[GIH][hapmap];0.94[TSI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3757527	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949293	chr7:6990891-7711883	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
2	nsv1026758	chr7:7187491-8075259	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
3	nsv606042	chr7:7427535-7876466	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats 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 lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
4	nsv887477	chr7:7531819-7810122	Weak transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
5	nsv1032670	chr7:7535515-8017077	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
6	nsv8043	chr7:7589195-7862802	Flanking Active TSS Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
7	nsv1034199	chr7:7617835-7691176	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
8	nsv606044	chr7:7652372-7727101	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
9	nsv887478	chr7:7670718-7917360	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
10	nsv887479	chr7:7681131-7779091	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
11	nsv887480	chr7:7681131-7917360	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
12	nsv887481	chr7:7681576-7779324	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
13	nsv887482	chr7:7682439-7785047	Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
14	nsv887483	chr7:7682439-7798217	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10254398	RADIL	cis	cerebellum	SCAN
rs10254398	COL28A1	cis	cerebellum	SCAN
rs10254398	MMD2	cis	parietal	SCAN

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:7681400-7688600	Weak transcription	Fetal Muscle Trunk	muscle
2	chr7:7681400-7688600	Weak transcription	Ovary	ovary
3	chr7:7681400-7690200	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr7:7681600-7692000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr7:7681600-7703800	Weak transcription	Stomach Mucosa	stomach
6	chr7:7681600-7710200	Weak transcription	Aorta	Aorta
7	chr7:7681800-7692600	Weak transcription	Primary T cells from cord blood	blood
8	chr7:7681800-7696400	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr7:7682000-7686800	Weak transcription	Right Ventricle	heart
10	chr7:7682000-7687200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr7:7682000-7687800	Weak transcription	Esophagus	oesophagus
12	chr7:7682000-7689400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
13	chr7:7682000-7690200	Weak transcription	Liver	Liver
14	chr7:7682000-7691000	Weak transcription	Fetal Kidney	kidney
15	chr7:7682000-7692600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr7:7682000-7694600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr7:7682000-7694600	Weak transcription	Primary neutrophils fromperipheralblood	blood
18	chr7:7682000-7694600	Weak transcription	Psoas Muscle	Psoas
19	chr7:7682000-7713800	Weak transcription	Left Ventricle	heart
20	chr7:7682200-7687000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr7:7682200-7687200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr7:7682200-7687200	Weak transcription	Primary T cells fromperipheralblood	blood
23	chr7:7682200-7711600	Weak transcription	Primary B cells from peripheral blood	blood
24	chr7:7682400-7691000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr7:7682600-7687400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
26	chr7:7682600-7687600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
27	chr7:7682600-7689000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
28	chr7:7682600-7689400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
29	chr7:7682600-7689600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
30	chr7:7682800-7689800	Weak transcription	Rectal Mucosa Donor 29	rectum
31	chr7:7683000-7687000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
32	chr7:7683600-7690400	Weak transcription	Rectal Mucosa Donor 31	rectum
33	chr7:7683800-7687600	Weak transcription	Primary T helper cells fromperipheralblood	blood
34	chr7:7685000-7686600	Strong transcription	Primary B cells from cord blood	blood
35	chr7:7685000-7687600	ZNF genes & repeats	Fetal Intestine Small	intestine
36	chr7:7685200-7689400	Weak transcription	Primary T helper cells PMA-I stimulated	--
37	chr7:7685600-7686600	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr7:7685600-7686600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
39	chr7:7685600-7686600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr7:7685600-7686600	ZNF genes & repeats	Fetal Thymus	thymus
41	chr7:7685600-7686600	Genic enhancers	Gastric	stomach
42	chr7:7685600-7686600	Strong transcription	Thymus	Thymus
43	chr7:7685600-7686600	ZNF genes & repeats	Dnd41	blood
44	chr7:7686000-7689600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr7:7686000-7691000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr7:7686200-7686600	ZNF genes & repeats	Fetal Stomach	stomach
47	chr7:7686400-7686600	ZNF genes & repeats	Pancreas	Pancrea
48	chr7:7686400-7688200	Enhancers	HepG2	liver
49	chr7:7686400-7690400	Weak transcription	Fetal Intestine Large	intestine

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