Variant report

Variant	rs2930946
Chromosome Location	chr5:68513004-68513005
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	MYC	chr5:68512987-68514383	K562	blood:	n/a	n/a
2	MXI1	chr5:68512978-68514252	Hela-S3	cervix:	n/a	chr5:68513460-68513469
3	SP1	chr5:68512950-68514379	A549	lung:	n/a	chr5:68513492-68513501 chr5:68513491-68513500 chr5:68513490-68513502 chr5:68513510-68513519 chr5:68513491-68513501 chr5:68514072-68514093 chr5:68513490-68513502 chr5:68513509-68513521 chr5:68513511-68513520 chr5:68513509-68513521 chr5:68513492-68513501 chr5:68513491-68513501
4	GTF3C2	chr5:68512503-68513397	Hela-S3	cervix:	n/a	n/a
5	MYC	chr5:68512874-68514341	K562	blood:	n/a	n/a
6	MAX	chr5:68512879-68513033	K562	blood:	n/a	n/a
7	MAZ	chr5:68512872-68514422	IMR90	lung:	n/a	n/a
8	MXI1	chr5:68512857-68514896	SK-N-SH	brain:	n/a	chr5:68513460-68513469
9	RCOR1	chr5:68512961-68513081	K562	blood:	n/a	n/a
10	POLR2A	chr5:68512821-68514440	SK-N-MC	brain:	n/a	n/a
11	EP300	chr5:68512998-68514243	K562	blood:	n/a	chr5:68513581-68513597 chr5:68513254-68513268
12	MAX	chr5:68512911-68514334	Hela-S3	cervix:	n/a	n/a
13	POLR2A	chr5:68512963-68513012	K562	blood:	n/a	n/a
14	POLR2A	chr5:68512862-68514369	K562	blood:	n/a	n/a
15	ESRRA	chr5:68512750-68514771	GM12878	blood:	n/a	chr5:68513502-68513515
16	ZNF384	chr5:68512327-68513466	K562	blood:	n/a	n/a
17	POLR2A	chr5:68512957-68514381	Hela-S3	cervix:	n/a	n/a
18	RFX5	chr5:68512903-68514397	Hela-S3	cervix:	n/a	chr5:68514074-68514083
19	POLR2A	chr5:68512961-68514388	K562	blood:	n/a	n/a
20	CTCF	chr5:68513000-68513150	GM06990	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:68471354..68475028-chr5:68512445..68515750,4	K562	blood:
2	chr5:68484254..68487485-chr5:68512131..68515372,4	K562	blood:
3	chr5:68512355..68516868-chr5:68528060..68533660,10	K562	blood:
4	chr5:68461458..68463761-chr5:68512888..68515184,2	MCF-7	breast:
5	chr5:68388388..68391466-chr5:68512032..68515267,4	MCF-7	breast:
6	chr5:68462643..68465474-chr5:68512138..68513918,2	K562	blood:
7	chr5:68512209..68515422-chr5:68529314..68532677,7	MCF-7	breast:
8	chr5:68512355..68517480-chr5:68528060..68532261,10	K562	blood:
9	chr5:68389720..68391335-chr5:68512201..68513725,2	MCF-7	breast:
10	chr5:68512009..68514181-chr5:68664891..68666779,2	MCF-7	breast:
11	chr5:68483023..68488056-chr5:68511952..68517380,10	K562	blood:
12	chr5:68511964..68513541-chr5:68626471..68628825,2	MCF-7	breast:
13	chr5:68512634..68513147-chr8:143781652..143782529,2	Hela-S3	cervix:

Variant related genes	Relation type
MRPS36	TF binding region
ENSG00000134058	Chromatin interaction
ENSG00000134057	Chromatin interaction
ENSG00000153044	Chromatin interaction
ENSG00000183323	Chromatin interaction
ENSG00000085231	Chromatin interaction
ENSG00000238334	Chromatin interaction
ENSG00000152942	Chromatin interaction
ENSG00000145740	Chromatin interaction
ENSG00000160886	Chromatin interaction

Extended variants
information (count: 100 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:97)

rs_ID	r²[population]
rs100192	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10940209	0.81[ASN][1000 genomes]
rs11742461	0.90[ASN][1000 genomes]
rs11744596	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11745578	0.90[ASN][1000 genomes]
rs11748974	0.80[ASN][1000 genomes]
rs12659146	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13175606	0.83[ASN][1000 genomes]
rs151589	0.83[ASN][1000 genomes]
rs163442	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs163443	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs163444	0.83[ASN][1000 genomes]
rs164386	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs164388	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs164389	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs164390	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs164715	0.83[ASN][1000 genomes]
rs1683831	0.92[ASN][1000 genomes]
rs184747	0.83[ASN][1000 genomes]
rs2002825	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2130757	0.81[ASN][1000 genomes]
rs2171148	0.81[ASN][1000 genomes]
rs2172056	0.81[ASN][1000 genomes]
rs2242351	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2291519	0.81[ASN][1000 genomes]
rs2291520	0.81[ASN][1000 genomes]
rs239591	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2450230	0.84[ASN][1000 genomes]
rs2637128	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2637129	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28506805	0.92[ASN][1000 genomes]
rs28576332	0.90[ASN][1000 genomes]
rs28693971	0.90[ASN][1000 genomes]
rs2913707	0.83[ASN][1000 genomes]
rs2930944	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2930945	0.85[ASN][1000 genomes]
rs2930949	0.81[ASN][1000 genomes]
rs2930951	0.81[ASN][1000 genomes]
rs2932770	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2932771	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2932772	0.85[ASN][1000 genomes]
rs2932773	0.85[ASN][1000 genomes]
rs2932775	0.85[ASN][1000 genomes]
rs2932776	0.85[ASN][1000 genomes]
rs2932777	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2932778	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2932780	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2932782	0.80[ASN][1000 genomes]
rs2932783	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2972358	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2972361	0.81[ASN][1000 genomes]
rs2972366	0.81[ASN][1000 genomes]
rs2972373	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2972374	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2972381	0.81[ASN][1000 genomes]
rs2972386	0.81[ASN][1000 genomes]
rs2972387	0.81[ASN][1000 genomes]
rs2972388	0.80[ASN][1000 genomes]
rs2972390	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34845020	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs350093	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs350094	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs350095	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs350099	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs350105	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs350107	0.83[ASN][1000 genomes]
rs350109	0.84[ASN][1000 genomes]
rs350115	0.83[ASN][1000 genomes]
rs350119	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs350120	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs350123	0.85[ASN][1000 genomes]
rs350124	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs350125	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs352626	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs353656	0.82[ASN][1000 genomes]
rs375285	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs376768	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs379434	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs386640	0.83[ASN][1000 genomes]
rs389686	0.92[ASN][1000 genomes]
rs389938	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs390169	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs395122	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs419902	0.83[ASN][1000 genomes]
rs4266362	0.82[ASN][1000 genomes]
rs437665	0.92[ASN][1000 genomes]
rs444305	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs476125	0.92[ASN][1000 genomes]
rs4976159	0.91[ASN][1000 genomes]
rs4976188	0.91[ASN][1000 genomes]
rs648489	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs651076	0.80[ASN][1000 genomes]
rs676879	0.81[ASN][1000 genomes]
rs6862253	0.89[ASN][1000 genomes]
rs693725	0.83[ASN][1000 genomes]
rs7719040	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs875459	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1018151	chr5:68377118-68667581	Enhancers Active TSS Flanking Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv1035004	chr5:68405526-68670101	Strong transcription Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
3	esv3378789	chr5:68438275-68540725	Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2930946	CCDC125	cis	Muscle Skeletal	GTEx
rs2930946	MRPS36	Cis_1M	lymphoblastoid	RTeQTL
rs2930946	CDK7	cis	Muscle Skeletal	GTEx

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:68486000-68513600	Weak transcription	Gastric	stomach
2	chr5:68490400-68513200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr5:68494600-68513200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr5:68495400-68513400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr5:68495600-68513200	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr5:68495600-68513400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr5:68497800-68513200	Weak transcription	Fetal Muscle Trunk	muscle
8	chr5:68502800-68513600	Weak transcription	Small Intestine	intestine
9	chr5:68507000-68513400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr5:68507400-68513400	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr5:68507600-68513200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr5:68508000-68513200	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr5:68508000-68513400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr5:68508000-68513400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr5:68509600-68513600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr5:68509800-68513400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr5:68510200-68513200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr5:68512400-68514600	Active TSS	Rectal Mucosa Donor 29	rectum
19	chr5:68512400-68514800	Active TSS	K562	blood
20	chr5:68512400-68515200	Active TSS	A549	lung
21	chr5:68512400-68515200	Active TSS	Hela-S3	cervix
22	chr5:68512600-68513400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr5:68512600-68514400	Active TSS	Duodenum Mucosa	Duodenum
24	chr5:68512600-68514600	Active TSS	GM12878-XiMat	blood
25	chr5:68512600-68514800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr5:68512800-68513200	Enhancers	Primary monocytes fromperipheralblood	blood
27	chr5:68512800-68513200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
28	chr5:68512800-68513200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
29	chr5:68512800-68513200	Enhancers	Right Ventricle	heart
30	chr5:68512800-68513400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr5:68512800-68514400	Active TSS	Breast Myoepithelial Primary Cells	Breast
32	chr5:68512800-68514400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr5:68512800-68514400	Active TSS	Placenta	Placenta
34	chr5:68512800-68514600	Active TSS	Primary hematopoietic stem cells short term culture	blood
35	chr5:68512800-68514600	Active TSS	Duodenum Smooth Muscle	Duodenum
36	chr5:68512800-68514600	Active TSS	Rectal Mucosa Donor 31	rectum
37	chr5:68512800-68514600	Active TSS	Rectal Smooth Muscle	rectum
38	chr5:68512800-68514800	Active TSS	Colonic Mucosa	Colon
39	chr5:68512800-68515200	Active TSS	ES-I3 Cell Line	embryonic stem cell
40	chr5:68513000-68513200	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr5:68513000-68513200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr5:68513000-68513200	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
43	chr5:68513000-68513200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr5:68513000-68513200	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr5:68513000-68513200	Flanking Active TSS	Primary B cells from peripheral blood	blood
46	chr5:68513000-68513200	Flanking Active TSS	Primary T cells from cord blood	blood
47	chr5:68513000-68513200	Flanking Active TSS	Primary hematopoietic stem cells	blood
48	chr5:68513000-68513200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
49	chr5:68513000-68513200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
50	chr5:68513000-68513200	Active TSS	Primary T regulatory cells fromperipheralblood	blood

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