Variant report

Variant	rs797680
Chromosome Location	chr1:93716974-93716975
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	KAP1	chr1:93716973-93717108	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:93716580..93719392-chr1:93724593..93726917,2	K562	blood:

Variant related genes	Relation type
CCDC18	TF binding region

Extended variants
information (count: 84 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs1010476	0.82[CHB][hapmap]
rs1060622	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs10782959	0.86[CHB][hapmap]
rs1088318	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11164870	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap]
rs11164876	0.91[CEU][hapmap];0.95[CHB][hapmap]
rs11164879	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs11164908	0.87[CHB][hapmap]
rs12030549	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs12030843	0.87[CHB][hapmap]
rs12033147	0.85[CHB][hapmap]
rs12038699	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap]
rs12044557	0.86[CHB][hapmap]
rs12044883	0.86[CEU][hapmap];0.95[CHB][hapmap]
rs12118262	0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs12128131	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.82[YRI][hapmap]
rs12133576	0.87[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap]
rs12406245	0.84[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap]
rs12563120	0.86[CHB][hapmap]
rs1335679	0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs1426318	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs1474927	0.96[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap]
rs1559828	0.87[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap]
rs1572343	0.91[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap]
rs1856027	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.82[YRI][hapmap]
rs1932314	1.00[YRI][hapmap];0.80[AMR][1000 genomes]
rs2031225	0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs2031226	0.87[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap]
rs2152358	0.80[AMR][1000 genomes]
rs2255722	0.82[CHB][hapmap]
rs2281524	0.82[CHB][hapmap]
rs2281525	0.83[CHB][hapmap]
rs2295423	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap]
rs2296558	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2391254	0.88[CEU][hapmap];1.00[CHB][hapmap]
rs2484486	0.81[CHB][hapmap]
rs2765545	0.91[CEU][hapmap];0.83[JPT][hapmap]
rs2783489	0.95[CHB][hapmap]
rs2783490	0.82[CHB][hapmap]
rs2783495	0.82[CHB][hapmap]
rs2783499	0.86[CHB][hapmap]
rs2783500	0.86[CHB][hapmap]
rs2783501	0.87[CHB][hapmap]
rs3754186	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs3767964	0.80[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap]
rs3904666	0.82[CHB][hapmap]
rs4000699	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs4240966	0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs4484937	0.86[CHB][hapmap]
rs4847235	0.91[CEU][hapmap];0.95[CHB][hapmap]
rs4847240	0.87[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap]
rs4847399	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap]
rs4847408	0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs531358	0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs535760	0.81[AMR][1000 genomes]
rs547866	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs565919	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs569414	0.91[CEU][hapmap]
rs602204	0.81[AMR][1000 genomes]
rs612037	1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs622608	1.00[CHB][hapmap];0.94[JPT][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs637646	1.00[CHB][hapmap];0.94[JPT][hapmap];0.83[AMR][1000 genomes]
rs6541349	0.90[CHB][hapmap];0.94[JPT][hapmap]
rs6541401	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs6541404	0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs6682670	0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs6703310	0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs682514	0.80[AMR][1000 genomes]
rs687394	1.00[CHB][hapmap];0.94[JPT][hapmap];0.83[AMR][1000 genomes]
rs693737	0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes]
rs7418101	0.83[AMR][1000 genomes]
rs7512911	0.83[AMR][1000 genomes]
rs7513705	0.88[CEU][hapmap];0.95[CHB][hapmap]
rs7517363	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs7525248	0.84[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap]
rs7535628	0.91[CEU][hapmap];0.95[CHB][hapmap]
rs7539307	0.88[CEU][hapmap];0.95[CHB][hapmap]
rs771481	0.91[CHB][hapmap]
rs797666	0.81[AMR][1000 genomes]
rs797668	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs797681	0.83[AMR][1000 genomes]
rs810027	0.82[CHB][hapmap]
rs942196	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830625	chr1:93566378-93735246	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs797680	RP4-717I23.3	cis	lung	GTEx
rs797680	RP4-717I23.3	cis	Whole Blood	GTEx
rs797680	TMED5	Cis_1M	lymphoblastoid	RTeQTL
rs797680	RP4-717I23.3	cis	Adipose Subcutaneous	GTEx
rs797680	RP4-717I23.3	cis	Esophagus Muscularis	GTEx
rs797680	RP4-717I23.3	cis	Artery Tibial	GTEx
rs797680	RP4-717I23.3	cis	Skin Sun Exposed Lower leg	GTEx
rs797680	RP4-717I23.3	cis	Esophagus Mucosa	GTEx
rs797680	RP4-717I23.3	cis	Muscle Skeletal	GTEx
rs797680	DR1	Cis_1M	lymphoblastoid	RTeQTL
rs797680	RP4-717I23.3	cis	Nerve Tibial	GTEx
rs797680	RP4-717I23.3	cis	Artery Aorta	GTEx
rs797680	RP4-717I23.3	cis	Thyroid	GTEx

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:93647000-93756400	Weak transcription	Gastric	stomach
2	chr1:93647200-93757600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr1:93666600-93727000	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr1:93690400-93729400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr1:93691200-93732400	Weak transcription	HUVEC	blood vessel
6	chr1:93692200-93787800	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr1:93704200-93729800	Weak transcription	Hela-S3	cervix
8	chr1:93706400-93727000	Weak transcription	K562	blood
9	chr1:93706600-93717200	Weak transcription	Primary T cells fromperipheralblood	blood
10	chr1:93707000-93727400	Weak transcription	Liver	Liver
11	chr1:93708800-93720200	Weak transcription	NHLF	lung
12	chr1:93709000-93717000	Weak transcription	Fetal Lung	lung
13	chr1:93709000-93717400	Weak transcription	Fetal Muscle Trunk	muscle
14	chr1:93709000-93717600	Weak transcription	Primary neutrophils fromperipheralblood	blood
15	chr1:93709000-93717600	Weak transcription	Ovary	ovary
16	chr1:93709000-93718200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr1:93709000-93718200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
18	chr1:93709000-93718400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr1:93709000-93718400	Weak transcription	Aorta	Aorta
20	chr1:93709000-93719000	Weak transcription	NHDF-Ad	bronchial
21	chr1:93709000-93719800	Weak transcription	HSMM	muscle
22	chr1:93709000-93720800	Weak transcription	Osteobl	bone
23	chr1:93709000-93724200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr1:93709000-93726400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr1:93709000-93727400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr1:93709000-93728200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr1:93709000-93728200	Weak transcription	HMEC	breast
28	chr1:93709200-93717600	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr1:93709200-93718200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr1:93709200-93718400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr1:93709200-93718400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
32	chr1:93709200-93718400	Weak transcription	Fetal Stomach	stomach
33	chr1:93709200-93727400	Weak transcription	Duodenum Mucosa	Duodenum
34	chr1:93709400-93718400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr1:93709400-93718400	Weak transcription	Fetal Thymus	thymus
36	chr1:93709400-93718400	Weak transcription	A549	lung
37	chr1:93709400-93727600	Weak transcription	Sigmoid Colon	Sigmoid Colon
38	chr1:93709600-93717400	Weak transcription	Fetal Intestine Small	intestine
39	chr1:93709600-93718200	Weak transcription	Primary T cells from cord blood	blood
40	chr1:93709600-93718400	Weak transcription	Primary monocytes fromperipheralblood	blood
41	chr1:93709600-93719000	Weak transcription	Primary T helper cells fromperipheralblood	blood
42	chr1:93709600-93720200	Weak transcription	Fetal Muscle Leg	muscle
43	chr1:93709600-93725000	Weak transcription	HepG2	liver
44	chr1:93709600-93725600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr1:93709600-93727000	Weak transcription	NHEK	skin
46	chr1:93709800-93718200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
47	chr1:93709800-93727000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr1:93709800-93727000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr1:93710000-93718200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr1:93710000-93718200	Weak transcription	Thymus	Thymus

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