Variant report

Variant	rs7550601
Chromosome Location	chr1:95088089-95088090
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	chr1:95080479..95082832-chr1:95086788..95088378,2	K562	blood:
2	chr1:95015461..95017197-chr1:95086412..95088142,2	K562	blood:

Extended variants
information (count: 23 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10782984	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11165185	1.00[CEU][hapmap];0.84[CHB][hapmap];0.97[GIH][hapmap];0.87[TSI][hapmap];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1343479	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1539151	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1539622	1.00[CEU][hapmap];0.84[CHB][hapmap];0.97[GIH][hapmap];0.87[TSI][hapmap];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1539623	1.00[CEU][hapmap];0.84[CHB][hapmap];0.97[GIH][hapmap];0.87[TSI][hapmap];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1620835	0.82[EUR][1000 genomes]
rs17111912	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1778196	0.81[EUR][1000 genomes]
rs1778218	0.84[EUR][1000 genomes]
rs2226095	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2996285	0.83[EUR][1000 genomes]
rs35360343	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3814017	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4351649	0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4847317	0.83[ASN][1000 genomes]
rs4847320	0.85[EUR][1000 genomes]
rs6661485	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7526391	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[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	nsv1001587	chr1:95027691-95318680	Weak transcription Strong transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
2	nsv947122	chr1:95081067-95089572	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv519997	chr1:95083836-95113417	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv1001230	chr1:95085184-95108531	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7550601	SNORD21	cis	parietal	SCAN
rs7550601	KIAA1107	cis	parietal	SCAN
rs7550601	MTF2	cis	parietal	SCAN

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:95075200-95088400	Weak transcription	Fetal Lung	lung
2	chr1:95082600-95088200	Weak transcription	HUES48 Cell Line	embryonic stem cell
3	chr1:95082800-95088200	Weak transcription	HUES64 Cell Line	embryonic stem cell
4	chr1:95083400-95088600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr1:95083800-95088600	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr1:95084000-95088200	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr1:95084800-95090200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr1:95085000-95090200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr1:95085000-95090600	Enhancers	HMEC	breast
10	chr1:95085200-95089600	Enhancers	Fetal Intestine Small	intestine
11	chr1:95085200-95089800	Enhancers	Breast Myoepithelial Primary Cells	Breast
12	chr1:95085200-95090000	Enhancers	NH-A	brain
13	chr1:95085200-95090600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr1:95085200-95090600	Enhancers	Placenta Amnion	Placenta Amnion
15	chr1:95085200-95090800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr1:95085400-95090000	Enhancers	Stomach Mucosa	stomach
17	chr1:95085600-95088200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr1:95085800-95089200	Enhancers	Esophagus	oesophagus
19	chr1:95085800-95089800	Enhancers	Fetal Intestine Large	intestine
20	chr1:95086200-95088600	Enhancers	Rectal Mucosa Donor 29	rectum
21	chr1:95086200-95088800	Enhancers	Fetal Heart	heart
22	chr1:95086200-95090600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr1:95086400-95089200	Enhancers	A549	lung
24	chr1:95086400-95090200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr1:95086600-95091200	Enhancers	ES-I3 Cell Line	embryonic stem cell
26	chr1:95086800-95089600	Enhancers	NHLF	lung
27	chr1:95086800-95090000	Enhancers	Placenta	Placenta
28	chr1:95087000-95088800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
29	chr1:95087000-95089800	Enhancers	HSMM	muscle
30	chr1:95087000-95089800	Enhancers	HSMMtube	muscle
31	chr1:95087000-95090200	Enhancers	NHEK	skin
32	chr1:95087200-95088200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr1:95087200-95088200	Weak transcription	Fetal Stomach	stomach
34	chr1:95087200-95088400	Weak transcription	Aorta	Aorta
35	chr1:95087200-95088400	Weak transcription	Gastric	stomach
36	chr1:95087200-95089000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr1:95087200-95089400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
38	chr1:95087200-95089400	Enhancers	Osteobl	bone
39	chr1:95087400-95088400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr1:95087600-95089800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr1:95087600-95090000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr1:95087600-95090000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr1:95087800-95088400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr1:95087800-95088400	Enhancers	Hela-S3	cervix
45	chr1:95087800-95088600	Weak transcription	NHDF-Ad	bronchial
46	chr1:95087800-95089800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr1:95087800-95089800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr1:95087800-95091000	Enhancers	HUES6 Cell Line	embryonic stem cell
49	chr1:95088000-95088800	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
50	chr1:95088000-95089000	Weak transcription	Fetal Kidney	kidney

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