Variant report

Variant	rs7040742
Chromosome Location	chr9:116784525-116784526
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	chr9:116778931..116781819-chr9:116782880..116785170,2	MCF-7	breast:

Extended variants
information (count: 24 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10739399	0.97[EUR][1000 genomes]
rs10759677	0.87[CEU][hapmap];0.97[EUR][1000 genomes]
rs10759678	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs10817553	0.93[EUR][1000 genomes]
rs10817557	1.00[CEU][hapmap];0.93[TSI][hapmap];0.98[EUR][1000 genomes]
rs1835731	0.98[EUR][1000 genomes]
rs1853546	0.85[TSI][hapmap]
rs1991706	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs2025391	0.82[GIH][hapmap]
rs2116406	1.00[CEU][hapmap];0.93[TSI][hapmap];0.98[EUR][1000 genomes]
rs2163575	0.98[EUR][1000 genomes]
rs4979316	0.83[TSI][hapmap];0.83[EUR][1000 genomes]
rs4979321	0.87[CEU][hapmap];0.90[TSI][hapmap];0.94[EUR][1000 genomes]
rs4979323	0.91[CEU][hapmap];0.97[EUR][1000 genomes]
rs4979324	0.87[CEU][hapmap];0.97[EUR][1000 genomes]
rs4979325	1.00[CEU][hapmap];0.93[TSI][hapmap];0.98[EUR][1000 genomes]
rs7023899	0.82[GIH][hapmap]
rs7023951	0.82[GIH][hapmap]
rs7026668	0.87[CEU][hapmap];0.97[EUR][1000 genomes]
rs7028504	0.94[EUR][1000 genomes]
rs7041487	0.87[CEU][hapmap];0.97[EUR][1000 genomes]
rs7042081	0.95[EUR][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	nsv430093	chr9:116330446-117325446	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	165 gene(s)	inside rSNPs	diseases
2	nsv521362	chr9:116782921-116785558	Weak transcription ZNF genes & repeats Strong transcription Enhancers	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7040742	SUSD1	cis	parietal	SCAN

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:116733400-116800200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr9:116764600-116797200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr9:116766000-116784800	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr9:116766000-116792600	Weak transcription	Stomach Mucosa	stomach
5	chr9:116766000-116798000	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr9:116766200-116799000	Weak transcription	Rectal Smooth Muscle	rectum
7	chr9:116766600-116811200	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr9:116767200-116785800	Weak transcription	Brain Cingulate Gyrus	brain
9	chr9:116768400-116794600	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr9:116768800-116784800	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr9:116769400-116790400	Weak transcription	Right Ventricle	heart
12	chr9:116773600-116809200	Weak transcription	Fetal Heart	heart
13	chr9:116774000-116791200	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr9:116774000-116791200	Weak transcription	Fetal Brain Male	brain
15	chr9:116774200-116798400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr9:116774600-116790400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr9:116775400-116784800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr9:116776200-116789800	Strong transcription	HUVEC	blood vessel
19	chr9:116777800-116785000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr9:116778000-116785200	Strong transcription	NHDF-Ad	bronchial
21	chr9:116778400-116785000	Strong transcription	Primary hematopoietic stem cells	blood
22	chr9:116778400-116785400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr9:116780200-116798600	Weak transcription	Colonic Mucosa	Colon
24	chr9:116780600-116796800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr9:116780800-116784800	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr9:116780800-116786800	Weak transcription	Left Ventricle	heart
27	chr9:116780800-116788000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr9:116780800-116788000	Weak transcription	Spleen	Spleen
29	chr9:116780800-116791000	Weak transcription	Gastric	stomach
30	chr9:116780800-116791000	Weak transcription	Pancreas	Pancrea
31	chr9:116780800-116791200	Weak transcription	Thymus	Thymus
32	chr9:116780800-116792800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr9:116780800-116796800	Weak transcription	Brain Angular Gyrus	brain
34	chr9:116780800-116798000	Weak transcription	Stomach Smooth Muscle	stomach
35	chr9:116780800-116800200	Weak transcription	Esophagus	oesophagus
36	chr9:116781000-116785000	Weak transcription	HUES6 Cell Line	embryonic stem cell
37	chr9:116781000-116785000	Weak transcription	Skeletal Muscle Female	skeletal muscle
38	chr9:116781000-116786800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr9:116781000-116787200	Weak transcription	NHLF	lung
40	chr9:116781000-116787800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr9:116781000-116790800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr9:116781000-116790800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr9:116781000-116797600	Weak transcription	Duodenum Mucosa	Duodenum
44	chr9:116781200-116785000	Weak transcription	HUES48 Cell Line	embryonic stem cell
45	chr9:116781200-116785000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
46	chr9:116781200-116788000	Weak transcription	Aorta	Aorta
47	chr9:116781400-116785200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr9:116781400-116786600	Weak transcription	Fetal Intestine Small	intestine
49	chr9:116781400-116786800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr9:116781400-116789200	Weak transcription	Skeletal Muscle Male	skeletal muscle

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