Variant report

Variant	rs4970993
Chromosome Location	chr1:151043850-151043851
allele	A/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	CTCF	chr1:151043521-151043881	T-47D	breast:	n/a	chr1:151043691-151043712 chr1:151043692-151043701 chr1:151043694-151043704 chr1:151043689-151043707 chr1:151043692-151043705 chr1:151043690-151043706 chr1:151043692-151043705
2	POLR2A	chr1:151042718-151043938	A549	lung:	n/a	n/a
3	CTCF	chr1:151043590-151043854	A549	lung:	n/a	chr1:151043691-151043712 chr1:151043692-151043701 chr1:151043694-151043704 chr1:151043689-151043707 chr1:151043692-151043705 chr1:151043690-151043706 chr1:151043692-151043705
4	TAL1	chr1:151042695-151043875	K562	blood:	n/a	n/a
5	MAZ	chr1:151042744-151043885	Hela-S3	cervix:	n/a	n/a
6	MTA3	chr1:151042554-151044152	GM12878	blood:	n/a	n/a
7	PML	chr1:151042465-151044102	GM12878	blood:	n/a	n/a
8	SIN3AK20	chr1:151042675-151043873	A549	lung:	n/a	n/a
9	TAF1	chr1:151042620-151043881	H1-hESC	embryonic stem cell:	n/a	n/a
10	MAX	chr1:151042635-151043971	ECC-1	luminal epithelium:	n/a	n/a
11	RAD21	chr1:151042763-151043953	H1-hESC	embryonic stem cell:	n/a	chr1:151042988-151042998 chr1:151043693-151043706 chr1:151043690-151043709
12	YY1	chr1:151042782-151043921	H1-hESC	embryonic stem cell:	n/a	chr1:151043647-151043658 chr1:151043701-151043710 chr1:151043698-151043707 chr1:151043747-151043758
13	YY1	chr1:151042561-151043855	SK-N-SH	brain:	n/a	chr1:151043647-151043658 chr1:151043701-151043710 chr1:151043698-151043707 chr1:151043747-151043758
14	CTCF	chr1:151042816-151043916	K562	blood:	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
15	RUNX3	chr1:151042659-151043934	GM12878	blood:	n/a	n/a
16	POLR2A	chr1:151042665-151043886	GM18526	blood:	n/a	n/a
17	EP300	chr1:151042753-151043907	K562	blood:	n/a	chr1:151043698-151043707
18	BCLAF1	chr1:151042641-151043923	GM12878	blood:	n/a	chr1:151043699-151043708 chr1:151043679-151043688 chr1:151043037-151043046
19	TEAD4	chr1:151042564-151043856	K562	blood:	n/a	n/a
20	MAX	chr1:151042644-151044025	MCF-7	breast:	n/a	n/a
21	POLR2A	chr1:151042668-151043930	ECC-1	luminal epithelium:	n/a	n/a
22	POLR2A	chr1:151042599-151043865	GM12891	blood:	n/a	n/a
23	CTCF	chr1:151043577-151043858	ECC-1	luminal epithelium:	n/a	chr1:151043691-151043712 chr1:151043692-151043701 chr1:151043694-151043704 chr1:151043689-151043707 chr1:151043692-151043705 chr1:151043690-151043706 chr1:151043692-151043705
24	POLR2A	chr1:151041429-151044042	PANC-1	pancreas:	n/a	n/a
25	ZNF143	chr1:151042824-151043857	H1-hESC	embryonic stem cell:	n/a	n/a
26	MAZ	chr1:151042713-151043975	GM12878	blood:	n/a	n/a
27	IRF1	chr1:151042728-151043866	K562	blood:	n/a	chr1:151043457-151043470 chr1:151043458-151043472
28	ZNF143	chr1:151042838-151043897	GM12878	blood:	n/a	n/a
29	POLR2A	chr1:151042487-151043892	GM19193	blood:	n/a	n/a
30	MAX	chr1:151042747-151043930	GM12878	blood:	n/a	n/a
31	POLR2A	chr1:151042582-151043963	GM12892	blood:	n/a	n/a
32	HEY1	chr1:151042559-151043853	K562	blood:	n/a	chr1:151043698-151043713
33	ETS1	chr1:151042665-151043931	A549	lung:	n/a	n/a
34	FOSL2	chr1:151042654-151043912	A549	lung:	n/a	n/a
35	HEY1	chr1:151042590-151043870	K562	blood:	n/a	chr1:151043698-151043713
36	TAF1	chr1:151042571-151043931	MCF-7	breast:	n/a	n/a
37	MYC	chr1:151042728-151043860	K562	blood:	n/a	n/a
38	NR2F2	chr1:151042561-151044593	K562	blood:	n/a	n/a
39	POLR2A	chr1:151042703-151043861	HCT-116	colon:	n/a	n/a
40	FOXM1	chr1:151042568-151044046	GM12878	blood:	n/a	n/a
41	TCF12	chr1:151042625-151043936	ECC-1	luminal epithelium:	n/a	n/a
42	MXI1	chr1:151042621-151043944	IMR90	lung:	n/a	n/a
43	SP1	chr1:151042777-151043885	H1-hESC	embryonic stem cell:	n/a	chr1:151043697-151043709 chr1:151043697-151043709
44	ATF2	chr1:151042705-151043899	H1-hESC	embryonic stem cell:	n/a	n/a
45	CTCF	chr1:151043592-151043853	HUVEC	blood vessel:	n/a	chr1:151043691-151043712 chr1:151043692-151043701 chr1:151043694-151043704 chr1:151043689-151043707 chr1:151043692-151043705 chr1:151043690-151043706 chr1:151043692-151043705
46	MYC	chr1:151042585-151043925	K562	blood:	n/a	n/a
47	YY1	chr1:151042702-151043887	K562	blood:	n/a	chr1:151043647-151043658 chr1:151043701-151043710 chr1:151043698-151043707 chr1:151043747-151043758
48	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
49	RELA	chr1:151042730-151043909	GM15510	blood:	n/a	n/a
50	CTCF	chr1:151043434-151043962	A549	lung:	n/a	chr1:151043691-151043712 chr1:151043692-151043701 chr1:151043694-151043704 chr1:151043689-151043707 chr1:151043692-151043705 chr1:151043690-151043706 chr1:151043692-151043705

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	chr1:150996741..150997636-chr1:151042895..151043878,5	MCF-7	breast:
6	chr1:151042193..151044467-chr1:151761804..151763901,2	MCF-7	breast:
7	chr1:150995604..150998641-chr1:151041475..151044833,5	MCF-7	breast:
8	chr1:151043637..151045310-chr1:151061634..151063146,2	MCF-7	breast:
9	chr1:150532621..150534705-chr1:151041557..151045135,3	K562	blood:
10	chr1:151000849..151004136-chr1:151043439..151047441,3	K562	blood:
11	chr1:150970397..150973154-chr1:151042388..151043902,2	MCF-7	breast:
12	chr1:151042976..151044739-chr1:151252844..151254871,2	K562	blood:
13	chr1:151043249..151044250-chr1:151127996..151129187,6	MCF-7	breast:
14	chr1:150978624..150980808-chr1:151042705..151044650,2	MCF-7	breast:
15	chr1:150996664..150997645-chr1:151043137..151044189,3	MCF-7	breast:
16	chr1:151043769..151044429-chr1:151128275..151128862,2	MCF-7	breast:
17	chr1:151031947..151032772-chr1:151043572..151044186,3	MCF-7	breast:
18	chr1:150978947..150982308-chr1:151041500..151045951,4	K562	blood:
19	chr1:150943930..150948676-chr1:151041268..151044275,5	MCF-7	breast:
20	chr1:151040998..151044328-chr1:151135769..151140484,5	MCF-7	breast:
21	chr1:151042160..151045059-chr1:151225748..151228568,3	MCF-7	breast:
22	chr1:151041683..151045028-chr1:151160226..151163233,4	MCF-7	breast:
23	chr1:151043837..151046087-chr1:151112231..151114471,2	K562	blood:
24	chr1:150944568..150948169-chr1:151041647..151044581,4	MCF-7	breast:
25	chr1:151040013..151045011-chr1:151111761..151118476,6	MCF-7	breast:
26	chr1:151042151..151045476-chr1:151127754..151130933,3	MCF-7	breast:
27	chr1:151042897..151044564-chr1:151161784..151163721,2	MCF-7	breast:
28	chr1:151042255..151044217-chr1:151136884..151138558,2	MCF-7	breast:

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

Extended variants
information (count: 54 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10749659	0.81[ASN][1000 genomes]
rs10788798	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10788799	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11204777	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11204778	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11204780	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11204782	1.00[JPT][hapmap]
rs11807526	1.00[JPT][hapmap]
rs12039334	0.81[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs12039542	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12040729	0.80[AFR][1000 genomes]
rs12087892	1.00[JPT][hapmap]
rs12117163	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12134957	0.81[ASN][1000 genomes]
rs12569193	0.86[JPT][hapmap]
rs1524773	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs15740	0.84[CEU][hapmap];0.80[EUR][1000 genomes]
rs1969442	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2067606	1.00[JPT][hapmap]
rs2140709	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2902810	0.89[CEU][hapmap];1.00[CHB][hapmap];0.84[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3738481	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3806386	0.89[CEU][hapmap];1.00[CHB][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3806387	0.89[CEU][hapmap];0.88[CHB][hapmap];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4357530	0.86[JPT][hapmap]
rs4512652	0.86[JPT][hapmap]
rs4970939	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4970941	0.86[JPT][hapmap]
rs4970998	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4970999	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4971002	0.84[ASN][1000 genomes]
rs4971003	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4971005	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4971006	0.84[ASN][1000 genomes]
rs4971007	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4971008	0.89[CEU][hapmap];1.00[JPT][hapmap]
rs6587553	0.94[CEU][hapmap];1.00[CHB][hapmap];0.84[YRI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6587557	0.86[JPT][hapmap]
rs6656450	0.86[JPT][hapmap]
rs6657593	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6668894	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6674970	0.86[JPT][hapmap]
rs6676190	1.00[JPT][hapmap]
rs6694158	1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7366148	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7523731	1.00[JPT][hapmap]
rs7532312	1.00[CHB][hapmap]
rs7540258	1.00[CHB][hapmap]
rs7550434	1.00[CHB][hapmap]
rs7554936	1.00[JPT][hapmap]

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
rs4970993	BNIPL	cis	Thyroid	GTEx
rs4970993	BNIPL	cis	lung	GTEx
rs4970993	LYSMD1	Cis_1M	lymphoblastoid	RTeQTL
rs4970993	CDC42SE1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151042200-151044000	Active TSS	iPS-15b Cell Line	embryonic stem cell
2	chr1:151042200-151044200	Active TSS	Colon Smooth Muscle	Colon
3	chr1:151042200-151044600	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr1:151042400-151044000	Active TSS	Breast Myoepithelial Primary Cells	Breast
5	chr1:151042400-151044000	Active TSS	Primary T cells from cord blood	blood
6	chr1:151042400-151044000	Active TSS	Primary T killer naive cells fromperipheralblood	blood
7	chr1:151042400-151044000	Active TSS	Fetal Intestine Large	intestine
8	chr1:151042400-151044000	Active TSS	Thymus	Thymus
9	chr1:151042400-151044200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr1:151042400-151044200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr1:151042400-151044200	Active TSS	Brain Substantia Nigra	brain
12	chr1:151042400-151044200	Active TSS	Pancreas	Pancrea
13	chr1:151042400-151044400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr1:151042400-151044600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr1:151042400-151044600	Active TSS	Rectal Mucosa Donor 29	rectum
16	chr1:151042600-151044000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
17	chr1:151042600-151044000	Active TSS	H1 Cell Line	embryonic stem cell
18	chr1:151042600-151044000	Active TSS	H9 Cell Line	embryonic stem cell
19	chr1:151042600-151044000	Active TSS	HUES6 Cell Line	embryonic stem cell
20	chr1:151042600-151044000	Active TSS	HUES64 Cell Line	embryonic stem cell
21	chr1:151042600-151044000	Active TSS	iPS-18 Cell Line	embryonic stem cell
22	chr1:151042600-151044000	Active TSS	iPS-20b Cell Line	embryonic stem cell
23	chr1:151042600-151044000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr1:151042600-151044000	Active TSS	Primary T helper naive cells from peripheral blood	blood
25	chr1:151042600-151044000	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
26	chr1:151042600-151044000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr1:151042600-151044000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr1:151042600-151044000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr1:151042600-151044000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
30	chr1:151042600-151044000	Active TSS	Esophagus	oesophagus
31	chr1:151042600-151044000	Active TSS	Fetal Stomach	stomach
32	chr1:151042600-151044000	Active TSS	Ovary	ovary
33	chr1:151042600-151044000	Active TSS	Psoas Muscle	Psoas
34	chr1:151042600-151044000	Active TSS	Rectal Mucosa Donor 31	rectum
35	chr1:151042600-151044000	Active TSS	Sigmoid Colon	Sigmoid Colon
36	chr1:151042600-151044000	Active TSS	Skeletal Muscle Male	skeletal muscle
37	chr1:151042600-151044000	Active TSS	HSMMtube	muscle
38	chr1:151042600-151044200	Active TSS	ES-I3 Cell Line	embryonic stem cell
39	chr1:151042600-151044200	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
40	chr1:151042600-151044200	Active TSS	Primary T killer memory cells from peripheral blood	blood
41	chr1:151042600-151044200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr1:151042600-151044200	Active TSS	Aorta	Aorta
43	chr1:151042600-151044200	Active TSS	Brain Cingulate Gyrus	brain
44	chr1:151042600-151044200	Active TSS	Brain Hippocampus Middle	brain
45	chr1:151042600-151044200	Active TSS	Brain Inferior Temporal Lobe	brain
46	chr1:151042600-151044200	Active TSS	Colonic Mucosa	Colon
47	chr1:151042600-151044200	Active TSS	Duodenum Mucosa	Duodenum
48	chr1:151042600-151044200	Active TSS	Fetal Kidney	kidney
49	chr1:151042600-151044200	Active TSS	Pancreatic Islets	Pancreatic Islet
50	chr1:151042600-151044200	Active TSS	Left Ventricle	heart

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