Variant report

Variant	rs633106
Chromosome Location	chr6:144605357-144605358
allele	A/C
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	FOXA2	chr6:144605326-144605626	HepG2	liver:	n/a	n/a
2	FOXA1	chr6:144605210-144605700	HepG2	liver:	n/a	n/a
3	CTCF	chr6:144605240-144605390	GM12865	blood:	n/a	chr6:144605307-144605316
4	CTCF	chr6:144605300-144605450	AG09309	skin:	n/a	chr6:144605307-144605316
5	MAX	chr6:144605199-144608606	HepG2	liver:	n/a	chr6:144605219-144605229 chr6:144605445-144605461 chr6:144607617-144607627 chr6:144608063-144608073 chr6:144605439-144605454
6	FOXA1	chr6:144605215-144605684	HepG2	liver:	n/a	n/a
7	CTCF	chr6:144605220-144605370	AG04449	skin:	n/a	chr6:144605307-144605316
8	CTCF	chr6:144605261-144605376	LNCaP	prostate:	n/a	chr6:144605307-144605316
9	CTCF	chr6:144605260-144605410	HPF	lung:	n/a	chr6:144605307-144605316
10	CTCF	chr6:144605280-144605430	GM12864	blood:	n/a	chr6:144605307-144605316
11	MYC	chr6:144605268-144606007	MCF10A-Er-Src	breast:	n/a	chr6:144605445-144605461 chr6:144605439-144605454
12	MAFK	chr6:144605296-144606127	HepG2	liver:	n/a	chr6:144605759-144605774 chr6:144605759-144605775
13	RAD21	chr6:144605133-144608594	IMR90	lung:	n/a	chr6:144606495-144606509 chr6:144605977-144605990 chr6:144606285-144606298
14	ZNF263	chr6:144604924-144608542	HEK293-T-REx	kidney:	n/a	chr6:144607029-144607038 chr6:144607880-144607889 chr6:144606409-144606418 chr6:144606412-144606421 chr6:144606416-144606437 chr6:144606415-144606424 chr6:144607284-144607293
15	CTCF	chr6:144605260-144605410	RPTEC	kidney:	n/a	chr6:144605307-144605316
16	CTCF	chr6:144605300-144605450	HMEC	breast:	n/a	chr6:144605307-144605316
17	CTCF	chr6:144605240-144605390	A549	lung:	n/a	chr6:144605307-144605316
18	CTCF	chr6:144605300-144605450	HMF	breast:	n/a	chr6:144605307-144605316
19	CTCF	chr6:144605220-144605370	MCF-7	breast:	n/a	chr6:144605307-144605316
20	CTCF	chr6:144605240-144605390	HA-sp	spinal cord:	n/a	chr6:144605307-144605316
21	KAP1	chr6:144604982-144607381	HEK293	kidney:	n/a	n/a
22	CTCF	chr6:144605220-144605370	HVMF	connective:	n/a	chr6:144605307-144605316
23	MAX	chr6:144605267-144608687	Hela-S3	cervix:	n/a	chr6:144605445-144605461 chr6:144607617-144607627 chr6:144608063-144608073 chr6:144605439-144605454
24	CTCF	chr6:144605220-144605370	HRPEpiC	eye:	n/a	chr6:144605307-144605316
25	CTCF	chr6:144605300-144605450	NHLF	lung:	n/a	chr6:144605307-144605316
26	CTCF	chr6:144605260-144605410	HFF-Myc	foreskin:	n/a	chr6:144605307-144605316
27	CTCF	chr6:144605260-144605410	HCM	heart:	n/a	chr6:144605307-144605316
28	CTCF	chr6:144605260-144605410	AoAF	blood vessel:	n/a	chr6:144605307-144605316
29	CTCF	chr6:144605220-144605370	GM12871	blood:	n/a	chr6:144605307-144605316
30	CTCF	chr6:144605220-144605370	SAEC	small airway:	n/a	chr6:144605307-144605316
31	ARID3A	chr6:144605324-144605524	K562	blood:	n/a	n/a
32	CTCF	chr6:144605220-144605370	SK-N-SH_RA	brain:	n/a	chr6:144605307-144605316
33	CTCF	chr6:144605260-144605410	BJ	skin:	n/a	chr6:144605307-144605316
34	POLR2A	chr6:144605330-144607776	HUVEC	blood vessel:	n/a	n/a
35	CTCF	chr6:144605240-144605390	AG04450	lung:	n/a	chr6:144605307-144605316
36	CTCF	chr6:144605260-144605410	HPAF	blood vessel:	n/a	chr6:144605307-144605316
37	MAFK	chr6:144605313-144606086	IMR90	lung:	n/a	chr6:144605759-144605774 chr6:144605759-144605775
38	MXI1	chr6:144605336-144608539	HepG2	liver:	n/a	n/a
39	CTCF	chr6:144605280-144605430	HCPEpiC	choroid plexus:	n/a	chr6:144605307-144605316
40	MAZ	chr6:144605014-144608603	IMR90	lung:	n/a	chr6:144605219-144605229 chr6:144605445-144605461 chr6:144607617-144607627 chr6:144608063-144608073 chr6:144605439-144605454
41	CTCF	chr6:144605240-144605390	HCFaa	heart:	n/a	chr6:144605307-144605316
42	CTCF	chr6:144605280-144605430	GM12875	blood:	n/a	chr6:144605307-144605316
43	CTCF	chr6:144605154-144605520	IMR90	lung:	n/a	chr6:144605307-144605316
44	CTCF	chr6:144605240-144605390	HPF	lung:	n/a	chr6:144605307-144605316
45	CTCF	chr6:144605240-144605390	HBMEC	blood vessel:	n/a	chr6:144605307-144605316
46	CTCF	chr6:144605238-144605387	HUVEC	blood vessel:	n/a	chr6:144605307-144605316
47	CTCF	chr6:144605240-144605390	NHDF-neo	bronchial:	n/a	chr6:144605307-144605316
48	CTCF	chr6:144605220-144605370	NHEK	skin:	n/a	chr6:144605307-144605316
49	MAFK	chr6:144605277-144606083	H1-hESC	embryonic stem cell:	n/a	chr6:144605759-144605774 chr6:144605759-144605775
50	MXI1	chr6:144605029-144609178	IMR90	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:144601184..144602939-chr6:144604140..144606671,2	K562	blood:
2	chr6:144605120..144606682-chr6:144616870..144619155,2	K562	blood:

Variant related genes	Relation type
UTRN	TF binding region

Extended variants
information (count: 62 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs2473129	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2473153	0.82[EUR][1000 genomes]
rs2502621	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs583341	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs583788	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs584283	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs586016	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs586471	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs586553	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs587691	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs587889	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs589892	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs590329	0.81[AFR][1000 genomes]
rs590362	0.88[AFR][1000 genomes]
rs591311	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs592388	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs592667	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs598222	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs599074	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs601816	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs601873	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs602764	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs603692	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs612928	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs615755	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs616619	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs619750	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs623320	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs632972	0.96[EUR][1000 genomes]
rs633802	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs637232	0.88[ASN][1000 genomes]
rs643596	0.92[EUR][1000 genomes]
rs644124	0.91[EUR][1000 genomes]
rs646837	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs647282	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs649426	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs652262	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs652765	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs658562	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs659899	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs660286	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs660307	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs660770	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs662419	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs664541	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs664721	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs665135	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs667740	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs667765	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs672468	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs676859	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs680093	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs681854	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs681916	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs682704	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs74671	0.88[EUR][1000 genomes]
rs849661	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830831	chr6:144501371-144649509	Bivalent/Poised TSS Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv830832	chr6:144572378-144759023	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers 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	6 gene(s)	inside rSNPs	diseases
3	esv2422260	chr6:144574591-144731630	Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Active TSS Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv1031253	chr6:144599055-144883013	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv538461	chr6:144599055-144883013	Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs633106	RP1-83M4.2	cis	Nerve Tibial	GTEx

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:144587800-144605800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr6:144600200-144605400	Weak transcription	Pancreas	Pancrea
3	chr6:144600200-144605400	Weak transcription	Skeletal Muscle Female	skeletal muscle
4	chr6:144601000-144605400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr6:144604200-144605400	Enhancers	Primary T killer memory cells from peripheral blood	blood
6	chr6:144604400-144605400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr6:144604600-144605400	Enhancers	Placenta	Placenta
8	chr6:144604800-144605400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr6:144604800-144605400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr6:144604800-144605400	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
11	chr6:144604800-144605600	Flanking Active TSS	Dnd41	blood
12	chr6:144604800-144608400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr6:144604800-144608800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr6:144604800-144608800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr6:144604800-144608800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr6:144604800-144609000	Active TSS	Brain Anterior Caudate	brain
17	chr6:144605000-144605400	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr6:144605000-144605400	Enhancers	Primary B cells from peripheral blood	blood
19	chr6:144605000-144605400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
20	chr6:144605000-144605400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
21	chr6:144605000-144605400	Enhancers	Colon Smooth Muscle	Colon
22	chr6:144605000-144605400	Flanking Active TSS	Fetal Stomach	stomach
23	chr6:144605000-144605400	Active TSS	Rectal Mucosa Donor 29	rectum
24	chr6:144605000-144605400	Enhancers	Stomach Mucosa	stomach
25	chr6:144605000-144605400	Bivalent/Poised TSS	GM12878-XiMat	blood
26	chr6:144605000-144605400	Flanking Active TSS	HSMM	muscle
27	chr6:144605000-144605600	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
28	chr6:144605000-144605600	Flanking Active TSS	Adipose Nuclei	Adipose
29	chr6:144605000-144605600	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
30	chr6:144605000-144605600	Flanking Active TSS	HMEC	breast
31	chr6:144605000-144605600	Flanking Active TSS	HUVEC	blood vessel
32	chr6:144605000-144605600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
33	chr6:144605000-144605600	Flanking Active TSS	NH-A	brain
34	chr6:144605000-144605600	Flanking Active TSS	Osteobl	bone
35	chr6:144605000-144605800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
36	chr6:144605000-144605800	Flanking Active TSS	Primary hematopoietic stem cells	blood
37	chr6:144605000-144605800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
38	chr6:144605000-144605800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr6:144605000-144605800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr6:144605000-144605800	Flanking Active TSS	NHEK	skin
41	chr6:144605000-144607200	Active TSS	H1 Cell Line	embryonic stem cell
42	chr6:144605000-144607400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr6:144605000-144607800	Active TSS	ES-I3 Cell Line	embryonic stem cell
44	chr6:144605000-144608600	Active TSS	Brain Hippocampus Middle	brain
45	chr6:144605000-144608800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr6:144605000-144608800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr6:144605000-144608800	Active TSS	Pancreatic Islets	Pancreatic Islet
48	chr6:144605000-144608800	Active TSS	Fetal Lung	lung
49	chr6:144605000-144608800	Active TSS	Right Atrium	heart
50	chr6:144605000-144608800	Active TSS	Right Ventricle	heart

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