Variant report

Variant	rs4970936
Chromosome Location	chr1:151044037-151044038
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	MTA3	chr1:151042554-151044152	GM12878	blood:	n/a	n/a
2	PML	chr1:151042465-151044102	GM12878	blood:	n/a	n/a
3	POLR2A	chr1:151041429-151044042	PANC-1	pancreas:	n/a	n/a
4	NR2F2	chr1:151042561-151044593	K562	blood:	n/a	n/a
5	FOXM1	chr1:151042568-151044046	GM12878	blood:	n/a	n/a
6	CTCF	chr1:151042688-151044091	MCF-7	breast:	n/a	chr1:151043691-151043712 chr1:151042992-151043001 chr1:151043692-151043701 chr1:151043694-151043704 chr1:151043689-151043707 chr1:151043692-151043705 chr1:151043690-151043706 chr1:151043692-151043705
7	ZBTB7A	chr1:151042657-151044038	ECC-1	luminal epithelium:	n/a	n/a
8	FOXA2	chr1:151044028-151044574	A549	lung:	n/a	n/a
9	MXI1	chr1:151042477-151044060	SK-N-SH	brain:	n/a	n/a
10	GTF3C2	chr1:151043697-151044481	Hela-S3	cervix:	n/a	n/a
11	POLR2A	chr1:151042505-151044073	GM12892	blood:	n/a	n/a
12	NR2F2	chr1:151042690-151044038	MCF-7	breast:	n/a	n/a
13	ELF1	chr1:151042591-151044043	MCF-7	breast:	n/a	chr1:151043707-151043719 chr1:151043907-151043919 chr1:151043223-151043236
14	GTF3C2	chr1:151041848-151044281	K562	blood:	n/a	n/a
15	FOXA1	chr1:151044013-151044406	HepG2	liver:	n/a	n/a
16	JUND	chr1:151042570-151044043	MCF-7	breast:	n/a	n/a
17	CTCF	chr1:151042482-151044041	SK-N-SH	brain:	n/a	chr1:151043691-151043712 chr1:151042992-151043001 chr1:151043692-151043701 chr1:151043694-151043704 chr1:151043689-151043707 chr1:151043692-151043705 chr1:151043690-151043706 chr1:151043692-151043705
18	POLR2A	chr1:151041723-151044343	K562	blood:	n/a	n/a
19	SIN3AK20	chr1:151042502-151044673	MCF-7	breast:	n/a	n/a
20	GABPA	chr1:151042620-151044044	MCF-7	breast:	n/a	n/a
21	POLR2A	chr1:151042371-151044074	PFSK-1	brain:	n/a	n/a
22	JUN	chr1:151041392-151045145	K562	blood:	n/a	chr1:151042028-151042035 chr1:151042007-151042017
23	RPC155	chr1:151043828-151044465	Hela-S3	cervix:	n/a	n/a
24	RCOR1	chr1:151042787-151044312	K562	blood:	n/a	n/a
25	POLR2A	chr1:151041597-151044082	GM12892	blood:	n/a	n/a
26	CHD1	chr1:151042478-151044625	IMR90	lung:	n/a	n/a
27	ZNF384	chr1:151043503-151044109	GM12878	blood:	n/a	n/a
28	HDAC2	chr1:151042607-151044047	MCF-7	breast:	n/a	chr1:151043416-151043430
29	MAZ	chr1:151042671-151044048	IMR90	lung:	n/a	n/a
30	CTCF	chr1:151042675-151045000	A549	lung:	n/a	chr1:151043691-151043712 chr1:151042992-151043001 chr1:151043692-151043701 chr1:151043694-151043704 chr1:151043689-151043707 chr1:151043692-151043705 chr1:151043690-151043706 chr1:151043692-151043705
31	FOXA2	chr1:151043967-151044389	A549	lung:	n/a	n/a
32	TCF12	chr1:151042537-151044506	A549	lung:	n/a	chr1:151044278-151044285
33	MAX	chr1:151042589-151044095	HCT-116	colon:	n/a	n/a
34	ZNF384	chr1:151041996-151044551	K562	blood:	n/a	n/a
35	SRF	chr1:151042680-151044049	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:150550567..150552845-chr1:151042071..151045056,2	MCF-7	breast:
2	chr1:151042356..151044958-chr1:151252271..151256325,4	K562	blood:
3	chr1:150977392..150983338-chr1:151040807..151046211,16	MCF-7	breast:
4	chr1:151043812..151045810-chr1:151065348..151067494,2	K562	blood:
5	chr1:151042193..151044467-chr1:151761804..151763901,2	MCF-7	breast:
6	chr1:150995604..150998641-chr1:151041475..151044833,5	MCF-7	breast:
7	chr1:151043637..151045310-chr1:151061634..151063146,2	MCF-7	breast:
8	chr1:150532621..150534705-chr1:151041557..151045135,3	K562	blood:
9	chr1:151000849..151004136-chr1:151043439..151047441,3	K562	blood:
10	chr1:151042976..151044739-chr1:151252844..151254871,2	K562	blood:
11	chr1:151043249..151044250-chr1:151127996..151129187,6	MCF-7	breast:
12	chr1:150978624..150980808-chr1:151042705..151044650,2	MCF-7	breast:
13	chr1:150996664..150997645-chr1:151043137..151044189,3	MCF-7	breast:
14	chr1:151043769..151044429-chr1:151128275..151128862,2	MCF-7	breast:
15	chr1:151031947..151032772-chr1:151043572..151044186,3	MCF-7	breast:
16	chr1:150978947..150982308-chr1:151041500..151045951,4	K562	blood:
17	chr1:150943930..150948676-chr1:151041268..151044275,5	MCF-7	breast:
18	chr1:151040998..151044328-chr1:151135769..151140484,5	MCF-7	breast:
19	chr1:151042160..151045059-chr1:151225748..151228568,3	MCF-7	breast:
20	chr1:151041683..151045028-chr1:151160226..151163233,4	MCF-7	breast:
21	chr1:151043837..151046087-chr1:151112231..151114471,2	K562	blood:
22	chr1:150944568..150948169-chr1:151041647..151044581,4	MCF-7	breast:
23	chr1:151040013..151045011-chr1:151111761..151118476,6	MCF-7	breast:
24	chr1:151042151..151045476-chr1:151127754..151130933,3	MCF-7	breast:
25	chr1:151042897..151044564-chr1:151161784..151163721,2	MCF-7	breast:
26	chr1:151042255..151044217-chr1:151136884..151138558,2	MCF-7	breast:

Variant related genes	Relation type
CDC42SE1	TF binding region
ENSG00000203288	Chromatin interaction
ENSG00000163156	Chromatin interaction
ENSG00000159352	Chromatin interaction
ENSG00000163159	Chromatin interaction
ENSG00000143373	Chromatin interaction
ENSG00000231073	Chromatin interaction
ENSG00000143458	Chromatin interaction
ENSG00000163155	Chromatin interaction
ENSG00000143409	Chromatin interaction
ENSG00000182134	Chromatin interaction
ENSG00000143418	Chromatin interaction
ENSG00000143434	Chromatin interaction
ENSG00000143363	Chromatin interaction
ENSG00000163154	Chromatin interaction
ENSG00000197622	Chromatin interaction
ENSG00000143384	Chromatin interaction
ENSG00000203804	Chromatin interaction
ENSG00000232671	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10749659	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10788800	0.85[ASN][1000 genomes]
rs11204771	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11204772	0.84[ASN][1000 genomes]
rs11204779	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12049116	0.87[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs12093562	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12134957	0.98[ASN][1000 genomes]
rs15740	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2902811	0.83[AMR][1000 genomes]
rs4357530	0.85[ASN][1000 genomes]
rs4360524	0.82[ASN][1000 genomes]
rs4970939	0.84[AMR][1000 genomes]
rs4970940	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4970941	0.88[ASN][1000 genomes]
rs61819219	0.85[ASN][1000 genomes]
rs6587552	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes]
rs6656450	0.85[ASN][1000 genomes]
rs6676190	0.85[ASN][1000 genomes]
rs6697617	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6704195	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7414477	0.83[ASN][1000 genomes]
rs7514185	0.85[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs7522608	0.93[ASN][1000 genomes]
rs7536234	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001897	chr1:150743271-151241600	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
2	nsv535158	chr1:150743271-151241600	Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
3	nsv522840	chr1:150933723-151347746	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	169 gene(s)	inside rSNPs	diseases
4	nsv916272	chr1:150961809-151557253	Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	219 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4970936	LYSMD1	Cis_1M	lymphoblastoid	RTeQTL
rs4970936	BNIPL	cis	Thyroid	GTEx
rs4970936	BNIPL	cis	lung	GTEx
rs4970936	CDC42SE1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151042200-151044200	Active TSS	Colon Smooth Muscle	Colon
2	chr1:151042200-151044600	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr1:151042400-151044200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr1:151042400-151044200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr1:151042400-151044200	Active TSS	Brain Substantia Nigra	brain
6	chr1:151042400-151044200	Active TSS	Pancreas	Pancrea
7	chr1:151042400-151044400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr1:151042400-151044600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr1:151042400-151044600	Active TSS	Rectal Mucosa Donor 29	rectum
10	chr1:151042600-151044200	Active TSS	ES-I3 Cell Line	embryonic stem cell
11	chr1:151042600-151044200	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
12	chr1:151042600-151044200	Active TSS	Primary T killer memory cells from peripheral blood	blood
13	chr1:151042600-151044200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr1:151042600-151044200	Active TSS	Aorta	Aorta
15	chr1:151042600-151044200	Active TSS	Brain Cingulate Gyrus	brain
16	chr1:151042600-151044200	Active TSS	Brain Hippocampus Middle	brain
17	chr1:151042600-151044200	Active TSS	Brain Inferior Temporal Lobe	brain
18	chr1:151042600-151044200	Active TSS	Colonic Mucosa	Colon
19	chr1:151042600-151044200	Active TSS	Duodenum Mucosa	Duodenum
20	chr1:151042600-151044200	Active TSS	Fetal Kidney	kidney
21	chr1:151042600-151044200	Active TSS	Pancreatic Islets	Pancreatic Islet
22	chr1:151042600-151044200	Active TSS	Left Ventricle	heart
23	chr1:151042600-151044200	Active TSS	NHDF-Ad	bronchial
24	chr1:151042600-151044400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr1:151042600-151044400	Active TSS	Brain Angular Gyrus	brain
26	chr1:151042600-151044400	Active TSS	Brain Anterior Caudate	brain
27	chr1:151042600-151044400	Active TSS	Duodenum Smooth Muscle	Duodenum
28	chr1:151042600-151044400	Active TSS	Fetal Brain Female	brain
29	chr1:151042600-151044400	Active TSS	Right Ventricle	heart
30	chr1:151042600-151044400	Active TSS	Osteobl	bone
31	chr1:151042600-151044800	Active TSS	NHLF	lung
32	chr1:151042800-151044200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr1:151042800-151044200	Active TSS	Fetal Intestine Small	intestine
34	chr1:151042800-151044200	Active TSS	Fetal Lung	lung
35	chr1:151042800-151044200	Active TSS	Gastric	stomach
36	chr1:151042800-151044200	Active TSS	Small Intestine	intestine
37	chr1:151042800-151044200	Active TSS	GM12878-XiMat	blood
38	chr1:151042800-151044200	Active TSS	HSMM	muscle
39	chr1:151042800-151044200	Active TSS	K562	blood
40	chr1:151042800-151044200	Active TSS	NHEK	skin
41	chr1:151042800-151044400	Active TSS	Lung	lung
42	chr1:151042800-151044400	Active TSS	Hela-S3	cervix
43	chr1:151043000-151044200	Active TSS	HMEC	breast
44	chr1:151043400-151044200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr1:151043600-151044200	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
46	chr1:151043600-151048200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr1:151043600-151048800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr1:151043600-151049600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr1:151043600-151050200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
50	chr1:151043800-151044200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived

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