Variant report

Variant	rs13238964
Chromosome Location	chr7:150062804-150062805
allele	A/G
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	POLR2A	chr7:150062773-150063518	HL-60	blood:	n/a	n/a

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

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

Extended variants
information (count: 49 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10248490	0.89[EUR][1000 genomes]
rs10259796	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10480297	0.83[ASN][1000 genomes]
rs1132261	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11767409	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11768108	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11773825	0.80[ASN][1000 genomes]
rs12703061	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13223702	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13307276	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17173681	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17173682	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17173702	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17173703	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1983441	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34311995	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34495356	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34728606	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35435439	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35635199	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35840727	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36035506	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs36069544	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs66688634	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6946097	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6946153	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs71537957	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs71537958	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7800196	0.90[EUR][1000 genomes];0.83[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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs13238964	LRRC61	cis	Nerve Tibial	GTEx
rs13238964	C7orf29	Cis_1M	lymphoblastoid	RTeQTL
rs13238964	REPIN1	cis	Muscle Skeletal	GTEx
rs13238964	LRRC61	cis	Thyroid	GTEx
rs13238964	LRRC61	cis	Muscle Skeletal	GTEx
rs13238964	LRRC61	cis	Skin Sun Exposed Lower leg	GTEx
rs13238964	ZBED6CL	cis	Esophagus Muscularis	GTEx

Chromatin state (count:73 , 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	chr7:150055200-150063000	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr7:150055200-150064800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr7:150055200-150065000	Weak transcription	Spleen	Spleen
6	chr7:150056400-150064800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr7:150056400-150064800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
8	chr7:150058600-150064800	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr7:150059000-150064800	Enhancers	Thymus	Thymus
10	chr7:150059000-150065200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr7:150059200-150064600	Enhancers	Primary B cells from cord blood	blood
12	chr7:150059200-150065000	Weak transcription	Psoas Muscle	Psoas
13	chr7:150059400-150063200	Enhancers	Skeletal Muscle Female	skeletal muscle
14	chr7:150059400-150065000	Enhancers	Primary B cells from peripheral blood	blood
15	chr7:150059600-150064800	Weak transcription	Rectal Smooth Muscle	rectum
16	chr7:150059800-150064200	Weak transcription	Liver	Liver
17	chr7:150059800-150064400	Weak transcription	HepG2	liver
18	chr7:150059800-150064800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr7:150059800-150065000	Weak transcription	Left Ventricle	heart
20	chr7:150060000-150064800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr7:150060200-150063200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr7:150060200-150065000	Enhancers	Primary monocytes fromperipheralblood	blood
23	chr7:150060200-150065000	Weak transcription	Fetal Heart	heart
24	chr7:150060400-150065000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr7:150060600-150064600	Enhancers	Primary T cells from cord blood	blood
26	chr7:150060600-150064800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr7:150060600-150065200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
28	chr7:150060800-150064800	Enhancers	Primary T helper cells fromperipheralblood	blood
29	chr7:150061000-150064400	Weak transcription	Pancreatic Islets	Pancreatic Islet
30	chr7:150061000-150065000	Weak transcription	Fetal Stomach	stomach
31	chr7:150061200-150064600	Enhancers	Primary hematopoietic stem cells	blood
32	chr7:150061200-150064800	Weak transcription	Brain Cingulate Gyrus	brain
33	chr7:150061200-150065000	Enhancers	Primary neutrophils fromperipheralblood	blood
34	chr7:150061200-150065000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr7:150061400-150063000	Weak transcription	H1 Cell Line	embryonic stem cell
36	chr7:150061400-150063000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr7:150061400-150063000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr7:150061400-150063000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr7:150061400-150064200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr7:150061400-150064600	Weak transcription	HUES64 Cell Line	embryonic stem cell
41	chr7:150061400-150064600	Weak transcription	Fetal Kidney	kidney
42	chr7:150061400-150064800	Weak transcription	Brain Anterior Caudate	brain
43	chr7:150061400-150064800	Weak transcription	HSMMtube	muscle
44	chr7:150061400-150065000	Weak transcription	HSMM	muscle
45	chr7:150061600-150063000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
46	chr7:150061600-150063000	Weak transcription	HUES48 Cell Line	embryonic stem cell
47	chr7:150061600-150063000	Weak transcription	Primary T helper cells PMA-I stimulated	--
48	chr7:150061600-150063000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
49	chr7:150061600-150063000	Weak transcription	K562	blood
50	chr7:150061600-150063200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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