Variant report

Variant	rs941289
Chromosome Location	chr7:99678491-99678492
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	chr7:99678449-99679676	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr7:99678454-99679773	H1-neurons	neurons:	n/a	n/a
3	GABPA	chr7:99678431-99679861	SK-N-SH	brain:	n/a	n/a
4	CTCF	chr7:99678430-99680094	A549	lung:	n/a	chr7:99679557-99679575 chr7:99679559-99679572 chr7:99679552-99679573 chr7:99679558-99679574 chr7:99679559-99679572
5	MAX	chr7:99678478-99679924	SK-N-SH	brain:	n/a	chr7:99679616-99679626
6	POLR2A	chr7:99677700-99679758	SK-N-SH	brain:	n/a	n/a
7	CREB1	chr7:99678479-99679818	HepG2	liver:	n/a	n/a
8	MAX	chr7:99678454-99679941	SK-N-SH	brain:	n/a	chr7:99679616-99679626
9	POLR2A	chr7:99678451-99679653	SK-N-SH	brain:	n/a	n/a
10	FOXA1	chr7:99678395-99679045	HepG2	liver:	n/a	chr7:99678632-99678647
11	NFIC	chr7:99678426-99678804	HepG2	liver:	n/a	n/a
12	ELF1	chr7:99678453-99678802	HepG2	liver:	n/a	chr7:99678662-99678673 chr7:99678661-99678674
13	SREBP2	chr7:99678395-99681082	GM12878	blood:	n/a	n/a
14	POLR2A	chr7:99678439-99679765	IMR90	lung:	n/a	n/a
15	POLR2A	chr7:99678481-99679794	GM12878	blood:	n/a	n/a
16	ARID3A	chr7:99678436-99679671	HepG2	liver:	n/a	n/a
17	GABPA	chr7:99678415-99679822	A549	lung:	n/a	n/a
18	GABPA	chr7:99678491-99679783	A549	lung:	n/a	n/a
19	MYBL2	chr7:99678413-99678843	HepG2	liver:	n/a	n/a
20	GABPA	chr7:99678402-99679958	MCF-7	breast:	n/a	n/a
21	POLR2A	chr7:99678480-99679745	GM12892	blood:	n/a	n/a
22	ELF1	chr7:99678445-99678861	HepG2	liver:	n/a	chr7:99678662-99678673 chr7:99678661-99678674
23	SIN3AK20	chr7:99678412-99679811	SK-N-SH	brain:	n/a	n/a
24	POLR2A	chr7:99678428-99679616	GM12878	blood:	n/a	n/a
25	TCF12	chr7:99678428-99679852	A549	lung:	n/a	chr7:99679475-99679485 chr7:99678760-99678768 chr7:99678719-99678726
26	POLR2A	chr7:99678473-99679511	HepG2	liver:	n/a	n/a
27	SMC3	chr7:99678235-99680005	SK-N-SH	brain:	n/a	chr7:99679559-99679573
28	NFIC	chr7:99678403-99678782	HepG2	liver:	n/a	n/a
29	GABPA	chr7:99678465-99679812	SK-N-SH	brain:	n/a	n/a
30	MYBL2	chr7:99678387-99679911	HepG2	liver:	n/a	n/a
31	MYC	chr7:99678404-99679870	A549	lung:	n/a	chr7:99679616-99679626
32	FOXA2	chr7:99678406-99678866	A549	lung:	n/a	n/a
33	SIX5	chr7:99678437-99679815	A549	lung:	n/a	n/a
34	FOXA2	chr7:99678456-99678943	HepG2	liver:	n/a	n/a
35	SIN3AK20	chr7:99678361-99680007	MCF-7	breast:	n/a	n/a
36	MAZ	chr7:99678447-99679995	IMR90	lung:	n/a	n/a
37	RAD21	chr7:99677612-99680025	SK-N-SH	brain:	n/a	chr7:99679559-99679573 chr7:99679555-99679574 chr7:99679115-99679125 chr7:99679557-99679569
38	POLR2A	chr7:99678233-99679742	HepG2	liver:	n/a	n/a
39	ELF1	chr7:99678456-99678869	K562	blood:	n/a	chr7:99678662-99678673 chr7:99678661-99678674
40	FOXA1	chr7:99678414-99678928	HepG2	liver:	n/a	chr7:99678632-99678647
41	REST	chr7:99678269-99679938	H1-neurons	neurons:	n/a	chr7:99679595-99679609 chr7:99679118-99679131 chr7:99679556-99679569 chr7:99679672-99679690 chr7:99679589-99679609
42	GABPA	chr7:99678396-99679856	MCF-7	breast:	n/a	n/a
43	POLR2A	chr7:99678398-99680650	H1-hESC	embryonic stem cell:	n/a	n/a
44	POLR2A	chr7:99678335-99679843	PFSK-1	brain:	n/a	n/a
45	POLR2A	chr7:99677580-99679844	SK-N-MC	brain:	n/a	n/a
46	MAX	chr7:99678453-99679854	HepG2	liver:	n/a	chr7:99679616-99679626
47	HEY1	chr7:99678448-99679782	HepG2	liver:	n/a	chr7:99679147-99679162
48	FOXA2	chr7:99678473-99678947	A549	lung:	n/a	n/a
49	MXI1	chr7:99676664-99679993	SK-N-SH	brain:	n/a	n/a
50	FOXA1	chr7:99678443-99678901	HepG2	liver:	n/a	chr7:99678632-99678647

No.	Distal block	Cell Line	Cell type
1	chr7:99611430..99615857-chr7:99675156..99681193,15	K562	blood:
2	chr7:99677846..99681399-chr7:100025174..100029012,4	K562	blood:
3	chr7:99576524..99578899-chr7:99677600..99679193,2	K562	blood:
4	chr7:99677781..99680960-chr7:99753334..99755747,3	K562	blood:
5	chr7:99643901..99648827-chr7:99678011..99681180,5	MCF-7	breast:
6	chr7:99515767..99517509-chr7:99677745..99680762,3	K562	blood:
7	chr7:99034954..99037975-chr7:99677842..99679932,3	K562	blood:
8	chr7:99612275..99615910-chr7:99677885..99681193,8	K562	blood:
9	chr7:99668310..99676246-chr7:99677185..99681836,16	MCF-7	breast:
10	chr7:99095910..99098991-chr7:99677831..99680952,3	K562	blood:
11	chr7:99677604..99679757-chr7:100032184..100034035,2	K562	blood:
12	chr7:99515562..99518077-chr7:99677870..99680297,2	MCF-7	breast:
13	chr7:99645911..99648901-chr7:99677073..99680526,5	MCF-7	breast:
14	chr7:99612316..99614498-chr7:99678113..99681049,2	MCF-7	breast:
15	chr7:99034954..99037866-chr7:99677567..99679393,3	K562	blood:
16	chr7:99678150..99680840-chr7:99745802..99747768,2	K562	blood:
17	chr7:99677060..99680949-chr7:100024846..100027547,5	MCF-7	breast:

Variant related genes	Relation type
ZNF3	TF binding region
ENSG00000166529	Chromatin interaction
ENSG00000241357	Chromatin interaction
ENSG00000266154	Chromatin interaction
ENSG00000146826	Chromatin interaction
ENSG00000240211	Chromatin interaction
ENSG00000146834	Chromatin interaction
ENSG00000214313	Chromatin interaction
ENSG00000146833	Chromatin interaction
ENSG00000106246	Chromatin interaction
ENSG00000160908	Chromatin interaction
ENSG00000166526	Chromatin interaction
ENSG00000160917	Chromatin interaction
ENSG00000188186	Chromatin interaction
ENSG00000160813	Chromatin interaction
ENSG00000078487	Chromatin interaction
ENSG00000106261	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs11558475	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11558476	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12532238	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12673441	0.90[MEX][hapmap];0.82[MKK][hapmap];0.85[ASN][1000 genomes]
rs2261360	0.90[MEX][hapmap];0.84[MKK][hapmap]
rs4308665	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4421299	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4727445	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4729573	0.83[ASN][1000 genomes]
rs4729575	0.82[JPT][hapmap];0.84[MKK][hapmap]
rs55969052	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56054049	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60697181	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6592	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs67091024	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67110214	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs68038211	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72615158	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72615159	0.85[ASN][1000 genomes]
rs7780686	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7796006	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7803317	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1829865	chr7:99430678-99755141	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1131 gene(s)	inside rSNPs	diseases
2	esv1830649	chr7:99430678-99755141	Strong transcription Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1131 gene(s)	inside rSNPs	diseases
3	nsv534298	chr7:99478011-99886076	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1132 gene(s)	inside rSNPs	diseases
4	nsv469687	chr7:99572543-99755141	Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1115 gene(s)	inside rSNPs	diseases
5	nsv482601	chr7:99572543-99755141	Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1115 gene(s)	inside rSNPs	diseases
6	nsv607931	chr7:99664817-99796146	Bivalent Enhancer Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Active TSS Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1097 gene(s)	inside rSNPs	diseases

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs941289	TRIM4	Cis_1M	lymphoblastoid	RTeQTL
rs941289	PILRB	Cis_1M	lymphoblastoid	RTeQTL
rs941289	PVRIG	Cis_1M	lymphoblastoid	RTeQTL
rs941289	PILRB	cis	parietal	SCAN
rs941289	AP4M1	cis	cerebellum	SCAN
rs941289	AP4M1	cis	Liver	GTEx
rs941289	LOC389541	Cis_1M	lymphoblastoid	RTeQTL
rs941289	TRIM4	cis	multi-tissue	Pritchard
rs941289	MCM7	cis	parietal	SCAN
rs941289	AP4M1	cis	multi-tissue	Pritchard
rs941289	MBLAC1	cis	cerebellum	SCAN
rs941289	MUC17	cis	parietal	SCAN
rs941289	PILRB	cis	multi-tissue	Pritchard
rs941289	OR2AE1	cis	parietal	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:99674800-99678600	Weak transcription	Aorta	Aorta
2	chr7:99675200-99678600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr7:99677000-99678600	Enhancers	Stomach Mucosa	stomach
4	chr7:99677400-99678600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
5	chr7:99677400-99678600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr7:99677400-99678600	Enhancers	Spleen	Spleen
7	chr7:99677600-99678600	Active TSS	HepG2	liver
8	chr7:99677600-99680400	Active TSS	iPS-15b Cell Line	embryonic stem cell
9	chr7:99677800-99678600	Enhancers	Primary B cells from peripheral blood	blood
10	chr7:99677800-99678600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
11	chr7:99677800-99678600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
12	chr7:99677800-99678600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
13	chr7:99677800-99678600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
14	chr7:99677800-99678600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
15	chr7:99677800-99678600	Enhancers	Esophagus	oesophagus
16	chr7:99677800-99678800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
17	chr7:99677800-99679000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr7:99677800-99679000	Flanking Active TSS	Adipose Nuclei	Adipose
19	chr7:99677800-99680600	Active TSS	ES-I3 Cell Line	embryonic stem cell
20	chr7:99678000-99678600	Enhancers	Primary neutrophils fromperipheralblood	blood
21	chr7:99678000-99678600	Flanking Active TSS	Brain Germinal Matrix	brain
22	chr7:99678000-99678600	Enhancers	Lung	lung
23	chr7:99678000-99678600	Active TSS	Rectal Mucosa Donor 29	rectum
24	chr7:99678000-99678600	Weak transcription	Small Intestine	intestine
25	chr7:99678000-99678800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
26	chr7:99678000-99678800	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
27	chr7:99678000-99679000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr7:99678000-99679000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr7:99678000-99679400	Active TSS	Sigmoid Colon	Sigmoid Colon
30	chr7:99678000-99679400	Active TSS	HSMMtube	muscle
31	chr7:99678000-99679400	Active TSS	NHLF	lung
32	chr7:99678000-99679600	Active TSS	HSMM	muscle
33	chr7:99678000-99679600	Active TSS	NH-A	brain
34	chr7:99678000-99679800	Active TSS	A549	lung
35	chr7:99678000-99680200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
36	chr7:99678000-99680400	Active TSS	H1 Cell Line	embryonic stem cell
37	chr7:99678000-99680400	Active TSS	HUES48 Cell Line	embryonic stem cell
38	chr7:99678000-99680400	Active TSS	HUES6 Cell Line	embryonic stem cell
39	chr7:99678000-99680400	Active TSS	HUES64 Cell Line	embryonic stem cell
40	chr7:99678000-99680400	Active TSS	iPS-18 Cell Line	embryonic stem cell
41	chr7:99678000-99680400	Active TSS	iPS-20b Cell Line	embryonic stem cell
42	chr7:99678000-99680400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr7:99678000-99680400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr7:99678000-99680400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
45	chr7:99678000-99680400	Active TSS	Fetal Kidney	kidney
46	chr7:99678000-99681000	Active TSS	H9 Cell Line	embryonic stem cell
47	chr7:99678200-99678600	Enhancers	Primary T killer memory cells from peripheral blood	blood
48	chr7:99678200-99678600	Flanking Active TSS	Duodenum Mucosa	Duodenum
49	chr7:99678200-99678800	Flanking Active TSS	Primary T cells from cord blood	blood
50	chr7:99678200-99678800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin

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