Variant report

Variant	rs664541
Chromosome Location	chr6:144608800-144608801
allele	C/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	GATA3	chr6:144607943-144608855	A549	lung:	n/a	chr6:144608278-144608287
2	MXI1	chr6:144605029-144609178	IMR90	lung:	n/a	n/a
3	RCOR1	chr6:144604958-144608817	IMR90	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:144608193..144609848-chr6:144615238..144616857,2	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	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2473153	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2502621	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs583341	0.93[CEU][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs583788	0.92[CEU][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs584283	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs586016	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs586471	0.92[CEU][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs586553	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs587691	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs587889	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs589892	1.00[CEU][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs590329	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs590362	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs591311	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs592388	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs592667	0.96[CEU][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs598222	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs599074	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs601816	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs601873	1.00[CEU][hapmap];0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs602764	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs603692	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs612928	0.92[CEU][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs615755	1.00[CEU][hapmap];0.90[YRI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs616619	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs619750	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs623320	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs632972	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs633106	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs633802	1.00[CEU][hapmap];0.95[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs637232	0.85[JPT][hapmap]
rs643596	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs644124	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs646837	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs647282	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs649426	0.96[CEU][hapmap];0.95[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs652262	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs652765	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs658562	0.93[EUR][1000 genomes]
rs659899	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs660286	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs660307	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs660770	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs662419	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs664721	0.93[CEU][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs665135	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs667740	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs667765	0.93[CEU][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs672468	1.00[CEU][hapmap];0.90[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs676859	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs680093	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs681854	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs681916	0.93[CEU][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs682704	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs74671	0.81[CEU][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs849661	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][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
rs664541	RP1-83M4.2	cis	Nerve Tibial	GTEx

Chromatin state (count:157 , 50 per page) page: 1 2 3 4

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:144604800-144608800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr6:144604800-144608800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr6:144604800-144608800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr6:144604800-144609000	Active TSS	Brain Anterior Caudate	brain
5	chr6:144605000-144608800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr6:144605000-144608800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr6:144605000-144608800	Active TSS	Pancreatic Islets	Pancreatic Islet
8	chr6:144605000-144608800	Active TSS	Fetal Lung	lung
9	chr6:144605000-144608800	Active TSS	Right Atrium	heart
10	chr6:144605000-144608800	Active TSS	Right Ventricle	heart
11	chr6:144605000-144608800	Active TSS	NHLF	lung
12	chr6:144605000-144609000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr6:144605000-144609000	Active TSS	Breast Myoepithelial Primary Cells	Breast
14	chr6:144605000-144609000	Active TSS	Ovary	ovary
15	chr6:144605000-144609000	Active TSS	Psoas Muscle	Psoas
16	chr6:144605000-144609600	Active TSS	Stomach Smooth Muscle	stomach
17	chr6:144605200-144608800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr6:144605200-144608800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr6:144605200-144608800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr6:144605200-144608800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr6:144605200-144608800	Active TSS	Fetal Kidney	kidney
22	chr6:144605200-144608800	Active TSS	Rectal Smooth Muscle	rectum
23	chr6:144605200-144609000	Active TSS	Aorta	Aorta
24	chr6:144605200-144609000	Active TSS	Brain Angular Gyrus	brain
25	chr6:144605200-144609000	Active TSS	Left Ventricle	heart
26	chr6:144605200-144609000	Active TSS	A549	lung
27	chr6:144605200-144609000	Active TSS	NHDF-Ad	bronchial
28	chr6:144605400-144608800	Active TSS	Fetal Intestine Large	intestine
29	chr6:144605400-144608800	Active TSS	Fetal Intestine Small	intestine
30	chr6:144605400-144608800	Active TSS	Fetal Muscle Leg	muscle
31	chr6:144605400-144608800	Active TSS	HSMM	muscle
32	chr6:144605400-144609000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr6:144605600-144608800	Active TSS	HUES6 Cell Line	embryonic stem cell
34	chr6:144605600-144608800	Active TSS	Muscle Satellite Cultured Cells	--
35	chr6:144605600-144608800	Active TSS	Brain Substantia Nigra	brain
36	chr6:144605600-144608800	Active TSS	Fetal Adrenal Gland	Adrenal Gland
37	chr6:144605600-144608800	Active TSS	Hela-S3	cervix
38	chr6:144605600-144608800	Active TSS	HMEC	breast
39	chr6:144605600-144608800	Active TSS	HSMMtube	muscle
40	chr6:144605600-144608800	Active TSS	Monocytes-CD14+_RO01746	blood
41	chr6:144605600-144608800	Active TSS	NH-A	brain
42	chr6:144605600-144609200	Active TSS	Duodenum Smooth Muscle	Duodenum
43	chr6:144605600-144609200	Active TSS	Sigmoid Colon	Sigmoid Colon
44	chr6:144605800-144608800	Active TSS	Rectal Mucosa Donor 29	rectum
45	chr6:144607000-144608800	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
46	chr6:144607000-144608800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
47	chr6:144607000-144609000	Flanking Active TSS	Primary hematopoietic stem cells	blood
48	chr6:144607200-144608800	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
49	chr6:144607200-144608800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
50	chr6:144607200-144608800	Flanking Bivalent TSS/Enh	Primary B cells from cord blood	blood

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