Variant report

Variant	rs28398138
Chromosome Location	chr7:150063151-150063152
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:8)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:8 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RCOR1	chr7:150062857-150063189	K562	blood:	n/a	n/a
2	EP300	chr7:150063055-150063505	GM12878	blood:	n/a	n/a
3	NFIC	chr7:150063085-150063407	GM12878	blood:	n/a	n/a
4	GATA3	chr7:150062882-150063441	T-47D	breast:	n/a	n/a
5	MXI1	chr7:150062990-150063290	GM12878	blood:	n/a	n/a
6	POLR2A	chr7:150062773-150063518	HL-60	blood:	n/a	n/a
7	TEAD4	chr7:150062853-150063565	K562	blood:	n/a	n/a
8	RELA	chr7:150063022-150063593	GM19099	blood:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:150061884..150064424-chr7:150091122..150093611,2	MCF-7	breast:
2	chr7:150016171..150021897-chr7:150062899..150068795,19	MCF-7	breast:
3	chr7:150037602..150039247-chr7:150062393..150064405,2	K562	blood:
4	chr7:72933491..72935453-chr7:150062419..150065143,2	MCF-7	breast:
5	chr7:150027152..150029852-chr7:150062347..150064947,2	K562	blood:

No data

Variant related genes	Relation type
ZNF775	TF binding region
REPIN1	TF binding region
ENSG00000127399	Chromatin interaction
ENSG00000106526	Chromatin interaction
ENSG00000261305	Chromatin interaction
ENSG00000106538	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10248975	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10264443	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10271869	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10278277	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1051760	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1051764	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1051823	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10952251	0.92[ASN][1000 genomes]
rs11771677	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11771693	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11972067	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1983441	0.87[EUR][1000 genomes]
rs3735165	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3735166	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3757423	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3757424	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3757425	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6722	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6946097	0.89[EUR][1000 genomes]
rs6946153	0.89[EUR][1000 genomes]
rs71537958	0.88[EUR][1000 genomes]
rs7800196	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9640161	0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:20 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1034409	chr7:149844639-150447071	Flanking Active TSS Active TSS Genic enhancers Enhancers ZNF genes & repeats Bivalent Enhancer Weak transcription Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
2	nsv608990	chr7:149961274-150707488	Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
3	nsv1015582	chr7:149967986-150285104	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
4	nsv889453	chr7:150009838-150104410	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
5	nsv889454	chr7:150009838-150115183	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
6	nsv889455	chr7:150013393-150104410	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
7	nsv889456	chr7:150013393-150115183	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
8	nsv1017368	chr7:150016952-150655773	Bivalent Enhancer ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
9	nsv539195	chr7:150016952-150655773	Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
10	nsv889457	chr7:150020295-150104410	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
11	nsv889458	chr7:150020295-150115183	Enhancers Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
12	nsv521407	chr7:150020295-150118590	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
13	nsv465211	chr7:150035526-150104410	Flanking Active TSS Active TSS Enhancers Genic enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
14	nsv608991	chr7:150035526-150104410	Flanking Active TSS Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
15	nsv889459	chr7:150041610-150071464	Enhancers Active TSS Strong transcription Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
16	nsv608992	chr7:150045910-150115183	Transcr. at gene 5' and 3' Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
17	esv1819714	chr7:150055837-150154944	Bivalent/Poised TSS Flanking Active TSS Active TSS Weak transcription Genic enhancers Strong transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
18	nsv889460	chr7:150060163-150079459	Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers Weak transcription Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
19	nsv889461	chr7:150060163-150081485	Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
20	nsv889462	chr7:150060163-150108536	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs28398138	C7orf29	Cis_1M	lymphoblastoid	RTeQTL
rs28398138	LRRC61	cis	Muscle Skeletal	GTEx
rs28398138	LRRC61	cis	Skin Sun Exposed Lower leg	GTEx
rs28398138	REPIN1	cis	Muscle Skeletal	GTEx

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:150039200-150065000	Weak transcription	Right Atrium	heart
2	chr7:150053200-150065000	Enhancers	Fetal Thymus	thymus
3	chr7:150055200-150064800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr7:150055200-150065000	Weak transcription	Spleen	Spleen
5	chr7:150056400-150064800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr7:150056400-150064800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
7	chr7:150058600-150064800	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr7:150059000-150064800	Enhancers	Thymus	Thymus
9	chr7:150059000-150065200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr7:150059200-150064600	Enhancers	Primary B cells from cord blood	blood
11	chr7:150059200-150065000	Weak transcription	Psoas Muscle	Psoas
12	chr7:150059400-150063200	Enhancers	Skeletal Muscle Female	skeletal muscle
13	chr7:150059400-150065000	Enhancers	Primary B cells from peripheral blood	blood
14	chr7:150059600-150064800	Weak transcription	Rectal Smooth Muscle	rectum
15	chr7:150059800-150064200	Weak transcription	Liver	Liver
16	chr7:150059800-150064400	Weak transcription	HepG2	liver
17	chr7:150059800-150064800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr7:150059800-150065000	Weak transcription	Left Ventricle	heart
19	chr7:150060000-150064800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr7:150060200-150063200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr7:150060200-150065000	Enhancers	Primary monocytes fromperipheralblood	blood
22	chr7:150060200-150065000	Weak transcription	Fetal Heart	heart
23	chr7:150060400-150065000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr7:150060600-150064600	Enhancers	Primary T cells from cord blood	blood
25	chr7:150060600-150064800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr7:150060600-150065200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
27	chr7:150060800-150064800	Enhancers	Primary T helper cells fromperipheralblood	blood
28	chr7:150061000-150064400	Weak transcription	Pancreatic Islets	Pancreatic Islet
29	chr7:150061000-150065000	Weak transcription	Fetal Stomach	stomach
30	chr7:150061200-150064600	Enhancers	Primary hematopoietic stem cells	blood
31	chr7:150061200-150064800	Weak transcription	Brain Cingulate Gyrus	brain
32	chr7:150061200-150065000	Enhancers	Primary neutrophils fromperipheralblood	blood
33	chr7:150061200-150065000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr7:150061400-150064200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr7:150061400-150064600	Weak transcription	HUES64 Cell Line	embryonic stem cell
36	chr7:150061400-150064600	Weak transcription	Fetal Kidney	kidney
37	chr7:150061400-150064800	Weak transcription	Brain Anterior Caudate	brain
38	chr7:150061400-150064800	Weak transcription	HSMMtube	muscle
39	chr7:150061400-150065000	Weak transcription	HSMM	muscle
40	chr7:150061600-150063200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr7:150061600-150063200	Weak transcription	Fetal Intestine Large	intestine
42	chr7:150061600-150063400	Weak transcription	Duodenum Mucosa	Duodenum
43	chr7:150061600-150064000	Weak transcription	Primary T cells fromperipheralblood	blood
44	chr7:150061600-150064000	Weak transcription	Fetal Muscle Leg	muscle
45	chr7:150061600-150064800	Weak transcription	HUVEC	blood vessel
46	chr7:150061600-150065000	Weak transcription	Brain Hippocampus Middle	brain
47	chr7:150061600-150065000	Weak transcription	Fetal Muscle Trunk	muscle
48	chr7:150061600-150065000	Weak transcription	Placenta	Placenta
49	chr7:150061800-150064200	Weak transcription	Adipose Nuclei	Adipose
50	chr7:150061800-150064400	Weak transcription	Skeletal Muscle Male	skeletal muscle

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