Variant report

Variant	rs35749329
Chromosome Location	chr15:56461133-56461134
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:56449170..56452087-chr15:56458652..56461237,3	K562	blood:
2	chr15:56460981..56464277-chr15:56465842..56468866,3	K562	blood:
3	chr15:56459962..56461531-chr15:56468857..56470997,2	K562	blood:

Extended variants
information (count: 66 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs11629483	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11631191	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12905899	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12907263	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12911094	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12911427	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12914260	0.82[EUR][1000 genomes]
rs12914640	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1372753	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1442640	0.87[EUR][1000 genomes]
rs1829542	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2119937	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2414464	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2460647	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2460648	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2460650	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2682044	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2682046	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2682049	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2682051	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2682053	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2682054	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2713923	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2713924	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2713926	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2713933	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2713936	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2713938	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2713941	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2718915	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2718941	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2725870	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34044869	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34144128	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34224072	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34386737	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34756325	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35082998	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35722267	0.82[EUR][1000 genomes]
rs35972806	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4310791	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4310792	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4774231	0.86[EUR][1000 genomes]
rs4774232	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4774847	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4774848	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs59432349	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62044082	0.83[EUR][1000 genomes]
rs62044110	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62044111	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6493835	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7165270	0.87[EUR][1000 genomes]
rs7168319	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7174823	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7175745	0.87[EUR][1000 genomes]
rs7496025	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8024031	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8028353	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8029114	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8032242	0.85[EUR][1000 genomes]
rs8033653	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9672886	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9672928	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833018	chr15:56325799-56492535	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv1045906	chr15:56333180-56473614	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
3	esv1811079	chr15:56448125-56462293	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs35749329	RFX7	cis	Adipose Subcutaneous	GTEx
rs35749329	RFX7	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:56433800-56464000	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr15:56435400-56462400	Weak transcription	Fetal Thymus	thymus
3	chr15:56435400-56465200	Weak transcription	Thymus	Thymus
4	chr15:56441000-56461400	Weak transcription	Monocytes-CD14+_RO01746	blood
5	chr15:56442000-56462600	Weak transcription	HSMM	muscle
6	chr15:56442600-56470600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr15:56442800-56462600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr15:56443200-56462600	Weak transcription	Duodenum Mucosa	Duodenum
9	chr15:56446600-56468400	Weak transcription	Fetal Lung	lung
10	chr15:56453000-56463200	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr15:56453000-56479600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr15:56453200-56462000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr15:56453200-56465000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr15:56453400-56463400	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr15:56453600-56515000	Weak transcription	NHLF	lung
16	chr15:56453800-56463000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr15:56454000-56462800	Weak transcription	Brain Germinal Matrix	brain
18	chr15:56454000-56464600	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr15:56454200-56465000	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr15:56454400-56462600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr15:56454400-56462600	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr15:56454400-56462600	Weak transcription	A549	lung
23	chr15:56454400-56463000	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr15:56454400-56464200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr15:56454400-56465000	Weak transcription	Fetal Stomach	stomach
26	chr15:56454400-56465600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr15:56454400-56466400	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr15:56454400-56467000	Weak transcription	Brain Angular Gyrus	brain
29	chr15:56454400-56467200	Weak transcription	Brain Cingulate Gyrus	brain
30	chr15:56454400-56470000	Weak transcription	Colon Smooth Muscle	Colon
31	chr15:56454400-56470200	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr15:56454400-56473400	Weak transcription	K562	blood
33	chr15:56454600-56463400	Weak transcription	HUES64 Cell Line	embryonic stem cell
34	chr15:56454600-56463400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
35	chr15:56454600-56465600	Weak transcription	Brain Substantia Nigra	brain
36	chr15:56454600-56484000	Weak transcription	Brain Anterior Caudate	brain
37	chr15:56454800-56465200	Weak transcription	Fetal Muscle Trunk	muscle
38	chr15:56455400-56462400	Weak transcription	Cortex derived primary cultured neurospheres	brain
39	chr15:56456000-56463400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr15:56456200-56462800	Weak transcription	Liver	Liver
41	chr15:56456600-56464800	Weak transcription	Stomach Smooth Muscle	stomach
42	chr15:56456600-56484800	Weak transcription	Aorta	Aorta
43	chr15:56456800-56463600	Weak transcription	Fetal Muscle Leg	muscle
44	chr15:56457200-56469000	Weak transcription	Hela-S3	cervix
45	chr15:56457400-56465000	Weak transcription	Fetal Intestine Small	intestine
46	chr15:56457400-56500400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr15:56457800-56462600	Weak transcription	Fetal Intestine Large	intestine
48	chr15:56457800-56463000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr15:56457800-56471600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr15:56458000-56470200	Weak transcription	Placenta Amnion	Placenta Amnion

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