Variant report

Variant	rs55974958
Chromosome Location	chr7:150037927-150037928
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:11)
CpG islands
(count:61)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:11 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	EGR1	chr7:150037500-150037953	K562	blood:	n/a	chr7:150037639-150037653
2	MAX	chr7:150036924-150037947	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr7:150032631-150038069	HepG2	liver:	n/a	n/a
4	POLR2A	chr7:150037858-150038049	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr7:150037120-150038162	HepG2	liver:	n/a	n/a
6	SIN3A	chr7:150037085-150038666	H1-hESC	embryonic stem cell:	n/a	n/a
7	E2F6	chr7:150037529-150037970	H1-hESC	embryonic stem cell:	n/a	n/a
8	MAX	chr7:150036997-150037972	H1-hESC	embryonic stem cell:	n/a	n/a
9	MAX	chr7:150036989-150038448	HepG2	liver:	n/a	n/a
10	CREB1	chr7:150037289-150037948	H1-hESC	embryonic stem cell:	n/a	n/a
11	EGR1	chr7:150037473-150037942	K562	blood:	n/a	chr7:150037639-150037653

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr7:150037890-150037940	SK-N-MC	brain:	n/a
2	chr7:150037890-150037940	AG10803	skin:	n/a
3	chr7:150037890-150037940	AG09319	gingival:	n/a
4	chr7:150037890-150037940	HEEpiC	esophagus:	n/a
5	chr7:150037890-150037940	HRPEpiC	eye:	n/a
6	chr7:150037890-150037940	HAEpiC	amniotic membrane:	n/a
7	chr7:150037890-150037940	LNCaP	prostate:	n/a
8	chr7:150037890-150037940	Hela-S3	cervix:	n/a
9	chr7:150037890-150037940	GM19239	blood:	n/a
10	chr7:150037890-150037940	ProgFib	skin:	n/a
11	chr7:150037890-150037940	HPAEpiC	pulmonary alveolar:	n/a
12	chr7:150037890-150037940	BJ	skin:	n/a
13	chr7:150037890-150037940	AoSMC	blood vessel:	n/a
14	chr7:150037890-150037940	HL-60	blood:	n/a
15	chr7:150037890-150037940	PrEC	prostate:	n/a
16	chr7:150037890-150037940	GM12892	blood:	n/a
17	chr7:150037890-150037940	NHBE	bronchial:	n/a
18	chr7:150037890-150037940	SK-N-SH	brain:	n/a
19	chr7:150037890-150037940	IMR90	lung:	fetal
20	chr7:150037890-150037940	GM12891	blood:	n/a
21	chr7:150037890-150037940	NH-A	brain:	n/a
22	chr7:150037890-150037940	CMK	blood:	n/a
23	chr7:150037890-150037940	PFSK-1	brain:	n/a
24	chr7:150037890-150037940	Hepatocyte	liver:	n/a
25	chr7:150037890-150037940	SKMC	muscle:	n/a
26	chr7:150037890-150037940	HEK293	kidney:	embryo
27	chr7:150037890-150037940	MCF10A-Er-Src	breast:	n/a
28	chr7:150037890-150037940	MCF-7	breast:	n/a
29	chr7:150037890-150037940	SAEC	small airway:	n/a
30	chr7:150037890-150037940	HRE	kidney:	n/a
31	chr7:150037890-150037940	RPTEC	kidney:	n/a
32	chr7:150037890-150037940	ovcar-3	ovarian:	n/a
33	chr7:150037890-150037940	GM06990	blood:	n/a
34	chr7:150037890-150037940	HCPEpiC	choroid plexus:	n/a
35	chr7:150037890-150037940	HNPCEpiC	eye:	n/a
36	chr7:150037890-150037940	ECC-1	luminal epithelium:	n/a
37	chr7:150037890-150037940	GM12878	blood:	n/a
38	chr7:150037890-150037940	AG04449	skin:	fetal
39	chr7:150037890-150037940	K562	blood:	n/a
40	chr7:150037890-150037940	Caco-2	colon:	n/a
41	chr7:150037890-150037940	BE2_C	brain:	n/a
42	chr7:150037890-150037940	SK-N-SH_RA	brain:	n/a
43	chr7:150037890-150037940	AG04450	lung:	fetal
44	chr7:150037890-150037940	Jurkat	blood:	n/a
45	chr7:150037890-150037940	HUVEC	blood vessel:	n/a
46	chr7:150037890-150037940	NB4	blood:	n/a
47	chr7:150037890-150037940	PANC-1	pancreas:	n/a
48	chr7:150037890-150037940	HRCEpiC	kidney:	n/a
49	chr7:150037890-150037940	HCM	heart:	n/a
50	chr7:150037890-150037940	AG09309	skin:	n/a

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

No.	Distal block	Cell Line	Cell type
1	chr7:150034163..150038835-chr7:150063325..150067223,6	MCF-7	breast:
2	chr7:150035327..150038333-chr7:150065389..150067921,3	MCF-7	breast:
3	chr7:150019150..150025305-chr7:150035524..150043799,10	MCF-7	breast:
4	chr7:150018389..150025798-chr7:150030734..150040389,17	MCF-7	breast:
5	chr7:150034829..150038326-chr7:150098733..150102665,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000261305	TF binding region
ENSG00000261305	CpG island
ENSG00000106526	Chromatin interaction
ENSG00000196456	Chromatin interaction
ENSG00000214022	Chromatin interaction
ENSG00000127399	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 20 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10282458	0.91[EUR][1000 genomes]
rs1047207	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1047575	0.85[EUR][1000 genomes]
rs1047586	0.85[EUR][1000 genomes]
rs10952250	0.83[EUR][1000 genomes]
rs10952252	0.90[EUR][1000 genomes]
rs11764936	0.91[EUR][1000 genomes]
rs11765644	0.92[EUR][1000 genomes]
rs11765692	0.84[EUR][1000 genomes]
rs11766288	0.82[EUR][1000 genomes]
rs11767726	0.81[EUR][1000 genomes]
rs11769348	0.91[EUR][1000 genomes]
rs11773351	0.92[EUR][1000 genomes]
rs11983355	0.81[EUR][1000 genomes]
rs1464752	0.82[EUR][1000 genomes]
rs1464753	0.84[EUR][1000 genomes]
rs17173617	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1916932	0.84[EUR][1000 genomes]
rs1962004	0.89[EUR][1000 genomes]
rs1983440	0.84[EUR][1000 genomes]
rs2098053	0.95[EUR][1000 genomes]
rs2108851	0.81[EUR][1000 genomes]
rs2108852	0.81[EUR][1000 genomes]
rs2108853	0.81[EUR][1000 genomes]
rs2108854	0.81[EUR][1000 genomes]
rs2159234	0.81[EUR][1000 genomes]
rs2159235	0.81[EUR][1000 genomes]
rs2159236	0.81[EUR][1000 genomes]
rs2373751	0.92[EUR][1000 genomes]
rs28432021	0.91[EUR][1000 genomes]
rs28439010	0.89[EUR][1000 genomes]
rs3088207	0.94[EUR][1000 genomes]
rs34489187	0.91[EUR][1000 genomes]
rs3735167	0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3735169	0.94[EUR][1000 genomes]
rs3735170	0.94[EUR][1000 genomes]
rs3735171	0.93[EUR][1000 genomes]
rs3735172	0.84[EUR][1000 genomes]
rs3735173	0.82[EUR][1000 genomes]
rs3735174	0.82[EUR][1000 genomes]
rs3735175	0.81[EUR][1000 genomes]
rs3800780	0.92[EUR][1000 genomes]
rs3800781	0.92[EUR][1000 genomes]
rs4395803	0.91[EUR][1000 genomes]
rs4554381	0.83[EUR][1000 genomes]
rs55881542	0.91[EUR][1000 genomes]
rs56190213	0.91[EUR][1000 genomes]
rs57888387	0.84[EUR][1000 genomes]
rs60268791	0.83[EUR][1000 genomes]
rs60283368	0.84[EUR][1000 genomes]
rs61421252	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs68107602	0.80[ASN][1000 genomes]
rs6964110	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73170169	0.84[EUR][1000 genomes]
rs73170174	0.81[EUR][1000 genomes]
rs73170185	0.92[EUR][1000 genomes]
rs73170192	0.90[EUR][1000 genomes]
rs883138	0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 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	nsv508490	chr7:150006068-150051241	Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	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

mRNA abundance (count:20)

SNP	Gene	Cis/trans	Tissue	Source
rs55974958	ZBED6CL	cis	Esophagus Muscularis	GTEx
rs55974958	ACTR3C	cis	Nerve Tibial	GTEx
rs55974958	LRRC61	Cis_1M	lymphoblastoid	RTeQTL
rs55974958	RP4-584D14.7	cis	Nerve Tibial	GTEx
rs55974958	ACTR3C	cis	Muscle Skeletal	GTEx
rs55974958	LRRC61	cis	Artery Tibial	GTEx
rs55974958	C7orf29	Cis_1M	lymphoblastoid	RTeQTL
rs55974958	LRRC61	cis	Artery Aorta	GTEx
rs55974958	REPIN1	cis	Muscle Skeletal	GTEx
rs55974958	LRRC61	cis	Heart Left Ventricle	GTEx
rs55974958	LRRC61	cis	Thyroid	GTEx
rs55974958	LRRC61	cis	Adipose Subcutaneous	GTEx
rs55974958	LRRC61	cis	lung	GTEx
rs55974958	LRRC61	cis	Nerve Tibial	GTEx
rs55974958	ZBED6CL	cis	Esophagus Mucosa	GTEx
rs55974958	LRRC61	cis	Whole Blood	GTEx
rs55974958	LRRC61	cis	Skin Sun Exposed Lower leg	GTEx
rs55974958	LRRC61	cis	Esophagus Mucosa	GTEx
rs55974958	LRRC61	cis	Muscle Skeletal	GTEx
rs55974958	RARRES2	cis	multi-tissue	Pritchard

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:150035600-150038000	Enhancers	Spleen	Spleen
2	chr7:150036000-150039200	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr7:150036200-150038400	Enhancers	GM12878-XiMat	blood
4	chr7:150036200-150038800	Bivalent Enhancer	Fetal Brain Male	brain
5	chr7:150036400-150038400	Enhancers	Primary hematopoietic stem cells short term culture	blood
6	chr7:150036400-150038600	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr7:150036600-150038000	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
8	chr7:150036600-150039200	Active TSS	Colon Smooth Muscle	Colon
9	chr7:150036800-150038000	Enhancers	Left Ventricle	heart
10	chr7:150036800-150038200	Flanking Active TSS	Pancreas	Pancrea
11	chr7:150036800-150038200	Flanking Active TSS	HSMM	muscle
12	chr7:150036800-150038600	Flanking Active TSS	Colonic Mucosa	Colon
13	chr7:150036800-150038600	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
14	chr7:150036800-150038600	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
15	chr7:150036800-150038800	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
16	chr7:150037000-150038000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr7:150037000-150038000	Bivalent Enhancer	Fetal Thymus	thymus
18	chr7:150037000-150038400	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
19	chr7:150037000-150038600	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
20	chr7:150037000-150038600	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
21	chr7:150037000-150038600	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
22	chr7:150037000-150038800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr7:150037000-150038800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr7:150037200-150038000	Enhancers	Placenta Amnion	Placenta Amnion
25	chr7:150037200-150038400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
26	chr7:150037200-150038400	Flanking Bivalent TSS/Enh	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr7:150037200-150038400	Flanking Active TSS	Right Ventricle	heart
28	chr7:150037200-150038600	Bivalent Enhancer	Primary B cells from peripheral blood	blood
29	chr7:150037200-150038600	Flanking Active TSS	Primary hematopoietic stem cells	blood
30	chr7:150037200-150038600	Active TSS	Small Intestine	intestine
31	chr7:150037400-150038000	Weak transcription	Brain Substantia Nigra	brain
32	chr7:150037400-150038000	Active TSS	Duodenum Smooth Muscle	Duodenum
33	chr7:150037400-150038200	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
34	chr7:150037400-150038200	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain
35	chr7:150037400-150038400	Active TSS	H9 Cell Line	embryonic stem cell
36	chr7:150037400-150038400	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
37	chr7:150037400-150038600	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
38	chr7:150037400-150038600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
39	chr7:150037400-150038600	Bivalent/Poised TSS	Sigmoid Colon	Sigmoid Colon
40	chr7:150037400-150038800	Active TSS	Liver	Liver
41	chr7:150037400-150038800	Active TSS	Fetal Kidney	kidney
42	chr7:150037400-150038800	Active TSS	Pancreatic Islets	Pancreatic Islet
43	chr7:150037400-150038800	Bivalent/Poised TSS	Fetal Stomach	stomach
44	chr7:150037400-150039000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
45	chr7:150037400-150039000	Bivalent/Poised TSS	Psoas Muscle	Psoas
46	chr7:150037400-150039200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
47	chr7:150037400-150039400	Active TSS	Rectal Smooth Muscle	rectum
48	chr7:150037600-150038000	Active TSS	iPS-20b Cell Line	embryonic stem cell
49	chr7:150037600-150038000	Enhancers	Brain Anterior Caudate	brain
50	chr7:150037600-150038000	Bivalent Enhancer	Brain Cingulate Gyrus	brain

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