Variant report

Variant	rs4844895
Chromosome Location	chr1:209958580-209958581
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	GABPA	chr1:209957715-209958602	K562	blood:	n/a	chr1:209957898-209957912 chr1:209957900-209957909 chr1:209957898-209957907 chr1:209957898-209957909 chr1:209957895-209957909
2	POLR2A	chr1:209957624-209958689	GM12891	blood:	n/a	n/a
3	GABPA	chr1:209957445-209958644	MCF-7	breast:	n/a	chr1:209957898-209957912 chr1:209957900-209957909 chr1:209957898-209957907 chr1:209957898-209957909 chr1:209957895-209957909
4	GABPA	chr1:209957574-209958656	A549	lung:	n/a	chr1:209957898-209957912 chr1:209957900-209957909 chr1:209957898-209957907 chr1:209957898-209957909 chr1:209957895-209957909
5	ZMIZ1	chr1:209957390-209958589	K562	blood:	n/a	n/a
6	POLR2A	chr1:209954531-209958662	K562	blood:	n/a	n/a
7	TCF7L2	chr1:209957833-209958586	PANC-1	pancreas:	n/a	n/a
8	REST	chr1:209957309-209958620	H1-neurons	neurons:	n/a	chr1:209958322-209958340 chr1:209957805-209957818 chr1:209958327-209958341 chr1:209957808-209957821 chr1:209958321-209958341 chr1:209957862-209957875 chr1:209957860-209957878
9	POLR2A	chr1:209957491-209958600	GM12878	blood:	n/a	n/a
10	POLR2A	chr1:209956429-209958657	GM19099	blood:	n/a	n/a
11	TBL1XR1	chr1:209957383-209958657	K562	blood:	n/a	n/a
12	PML	chr1:209957343-209958595	K562	blood:	n/a	n/a
13	MAX	chr1:209957406-209958620	NB4	blood:	n/a	chr1:209957805-209957814
14	POLR2A	chr1:209957453-209958705	GM12892	blood:	n/a	n/a
15	NFIC	chr1:209957403-209958649	GM12878	blood:	n/a	n/a
16	CREB1	chr1:209957473-209958637	GM12878	blood:	n/a	chr1:209957942-209957955
17	CUX1	chr1:209957604-209958594	K562	blood:	n/a	n/a
18	POLR2A	chr1:209957533-209958650	GM12891	blood:	n/a	n/a
19	CBX3	chr1:209957472-209958679	K562	blood:	n/a	chr1:209957492-209957503
20	POLR2A	chr1:209957498-209958933	GM12878	blood:	n/a	n/a
21	POLR2A	chr1:209957405-209958850	PBDE	blood:	n/a	n/a
22	POLR2A	chr1:209956681-209958618	Raji	blood:	n/a	n/a
23	POLR2A	chr1:209952928-209958954	GM12878	blood:	n/a	n/a
24	TCF12	chr1:209957473-209958602	A549	lung:	n/a	chr1:209958138-209958148
25	POLR2A	chr1:209956724-209958657	K562	blood:	n/a	n/a
26	SPI1	chr1:209957755-209958618	HL-60	blood:	n/a	n/a
27	GABPA	chr1:209957460-209958643	A549	lung:	n/a	chr1:209957898-209957912 chr1:209957900-209957909 chr1:209957898-209957907 chr1:209957898-209957909 chr1:209957895-209957909
28	PML	chr1:209957421-209958636	K562	blood:	n/a	n/a
29	TBL1XR1	chr1:209957488-209958586	GM12878	blood:	n/a	n/a
30	SETDB1	chr1:209957769-209958606	K562	blood:	n/a	chr1:209957899-209957908
31	KAP1	chr1:209958006-209958905	K562	blood:	n/a	n/a
32	POLR2A	chr1:209957551-209958581	GM18505	blood:	n/a	n/a
33	MAX	chr1:209957393-209958662	A549	lung:	n/a	chr1:209957805-209957814
34	HCFC1	chr1:209957118-209958766	Hela-S3	cervix:	n/a	n/a
35	USF2	chr1:209957412-209958746	GM12878	blood:	n/a	n/a
36	CHD2	chr1:209957394-209958582	K562	blood:	n/a	n/a
37	MAX	chr1:209957556-209958650	SK-N-SH	brain:	n/a	chr1:209957805-209957814
38	BACH1	chr1:209957609-209958583	K562	blood:	n/a	n/a
39	E2F6	chr1:209957426-209958677	A549	lung:	n/a	chr1:209958132-209958139 chr1:209957943-209957952 chr1:209958132-209958139 chr1:209957593-209957603 chr1:209957945-209957954 chr1:209958132-209958139 chr1:209957899-209957908
40	RCOR1	chr1:209957605-209958654	GM12878	blood:	n/a	n/a
41	IRF1	chr1:209957279-209958673	K562	blood:	n/a	chr1:209957594-209957608 chr1:209957344-209957358
42	POLR2A	chr1:209957500-209958589	HCT-116	colon:	n/a	n/a
43	POLR2A	chr1:209956778-209958666	H1-hESC	embryonic stem cell:	n/a	n/a
44	POLR2A	chr1:209957465-209958681	MCF10A-Er-Src	breast:	n/a	n/a
45	CBX3	chr1:209957812-209958587	K562	blood:	n/a	n/a
46	NRF1	chr1:209957701-209958604	Hela-S3	cervix:	n/a	chr1:209957898-209957912 chr1:209957897-209957908 chr1:209957900-209957909 chr1:209957898-209957907 chr1:209957898-209957909 chr1:209957895-209957909
47	MAX	chr1:209957458-209958628	K562	blood:	n/a	chr1:209957805-209957814
48	POLR2A	chr1:209952746-209958845	GM12891	blood:	n/a	n/a
49	REST	chr1:209957627-209958608	HL-60	blood:	n/a	chr1:209958322-209958340 chr1:209957805-209957818 chr1:209958327-209958341 chr1:209957808-209957821 chr1:209958321-209958341 chr1:209957862-209957875 chr1:209957860-209957878
50	JUND	chr1:209957239-209958696	SK-N-SH	brain:	n/a	chr1:209957944-209957953

No.	Distal block	Cell Line	Cell type
1	chr1:209955222..209959394-chr1:210545816..210547914,4	K562	blood:
2	chr1:209946631..209949857-chr1:209956266..209959109,3	MCF-7	breast:
3	chr1:209957820..209958586-chr4:100871003..100871812,2	Hela-S3	cervix:
4	chr1:209955520..209962214-chr1:209976009..209982555,8	K562	blood:
5	chr1:209940429..209942619-chr1:209957623..209959222,2	MCF-7	breast:
6	chr1:209957348..209959526-chr1:209965730..209967837,2	K562	blood:
7	chr1:209950429..209953463-chr1:209956092..209959569,7	K562	blood:
8	chr1:209957965..209959806-chr1:209959959..209962744,2	K562	blood:
9	chr1:209954505..209956563-chr1:209958183..209960148,2	K562	blood:
10	chr1:209957266..209960368-chr1:209964452..209967778,3	MCF-7	breast:
11	chr1:209955602..209959674-chr1:209962858..209967873,6	MCF-7	breast:
12	chr1:209956289..209959543-chr1:209978892..209981541,4	K562	blood:

Variant related genes	Relation type
C1orf74	TF binding region
ENSG00000164032	Chromatin interaction
ENSG00000245322	Chromatin interaction
ENSG00000009790	Chromatin interaction
ENSG00000232222	Chromatin interaction
ENSG00000117595	Chromatin interaction
ENSG00000200972	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1044516	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.83[LWK][hapmap];0.94[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11803382	0.87[EUR][1000 genomes]
rs11805830	0.87[EUR][1000 genomes]
rs12070337	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1319072	0.82[TSI][hapmap]
rs1415543	0.86[TSI][hapmap]
rs17015183	0.84[EUR][1000 genomes]
rs17015218	0.86[ASW][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes]
rs17015224	0.87[EUR][1000 genomes]
rs17015226	0.86[ASW][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes]
rs17015259	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17015309	0.91[TSI][hapmap]
rs17015379	0.82[TSI][hapmap]
rs17317411	0.91[TSI][hapmap];0.82[EUR][1000 genomes]
rs2073485	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2235372	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2235373	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3753518	0.87[EUR][1000 genomes]
rs41305104	0.81[EUR][1000 genomes]
rs4556361	0.86[TSI][hapmap]
rs58637469	0.87[EUR][1000 genomes]
rs6540559	1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6540560	0.86[ASW][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes]
rs6540561	0.87[EUR][1000 genomes]
rs6694552	0.87[EUR][1000 genomes]
rs6696825	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs742214	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs742215	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.94[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7522250	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7525951	0.86[TSI][hapmap]
rs7539638	0.82[TSI][hapmap]
rs7550857	0.86[ASW][hapmap];0.86[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes]
rs764093	1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs926346	0.87[EUR][1000 genomes]
rs926347	0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999901	chr1:209600631-210205379	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	nsv1014034	chr1:209759648-210501731	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv873139	chr1:209828955-210050794	Active TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv1006632	chr1:209886202-209970355	Flanking Active TSS Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
5	nsv4343	chr1:209929932-209974877	Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
6	nsv1067914	chr1:209955818-209972979	Enhancers Transcr. at gene 5' and 3' Weak transcription Genic enhancers Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	n/a
7	nsv945273	chr1:209958252-209960036	Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	n/a

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs4844895	LPGAT1	cis	cerebellum	SCAN
rs4844895	IRF6	cis	cerebellum	SCAN
rs4844895	G0S2	cis	parietal	SCAN
rs4844895	SYT14	cis	parietal	SCAN
rs4844895	TRAF3IP3	cis	Whole Blood	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:209956800-209958600	Active TSS	HUES6 Cell Line	embryonic stem cell
2	chr1:209956800-209958600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
3	chr1:209956800-209958600	Active TSS	HSMM	muscle
4	chr1:209957000-209958600	Active TSS	HUES48 Cell Line	embryonic stem cell
5	chr1:209957000-209958600	Active TSS	HUES64 Cell Line	embryonic stem cell
6	chr1:209957000-209958600	Active TSS	Brain Germinal Matrix	brain
7	chr1:209957000-209958600	Active TSS	Fetal Kidney	kidney
8	chr1:209957200-209958600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr1:209957200-209958600	Flanking Active TSS	Primary T cells fromperipheralblood	blood
10	chr1:209957200-209958600	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr1:209957200-209958600	Active TSS	HSMMtube	muscle
12	chr1:209957200-209958800	Active TSS	Duodenum Smooth Muscle	Duodenum
13	chr1:209957400-209958600	Flanking Active TSS	Primary B cells from peripheral blood	blood
14	chr1:209957400-209958600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
15	chr1:209957400-209958600	Active TSS	Brain Inferior Temporal Lobe	brain
16	chr1:209957400-209958600	Active TSS	Fetal Brain Female	brain
17	chr1:209957400-209958600	Active TSS	Sigmoid Colon	Sigmoid Colon
18	chr1:209957400-209958600	Active TSS	Skeletal Muscle Female	skeletal muscle
19	chr1:209957600-209958600	Active TSS	Brain Angular Gyrus	brain
20	chr1:209957600-209958600	Active TSS	Brain Anterior Caudate	brain
21	chr1:209957600-209958600	Active TSS	Fetal Brain Male	brain
22	chr1:209957800-209978600	Weak transcription	Spleen	Spleen
23	chr1:209958000-209958600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
24	chr1:209958000-209958600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
25	chr1:209958000-209958600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr1:209958000-209958600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
27	chr1:209958000-209958600	Flanking Active TSS	Fetal Heart	heart
28	chr1:209958000-209958600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
29	chr1:209958000-209958600	Flanking Active TSS	Stomach Smooth Muscle	stomach
30	chr1:209958000-209958600	Flanking Active TSS	Osteobl	bone
31	chr1:209958000-209958800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
32	chr1:209958000-209958800	Flanking Active TSS	Dnd41	blood
33	chr1:209958000-209960600	Weak transcription	Placenta Amnion	Placenta Amnion
34	chr1:209958000-209961000	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr1:209958000-209961400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr1:209958000-209971600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr1:209958200-209958600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr1:209958200-209958600	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr1:209958200-209958600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr1:209958200-209958600	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr1:209958200-209958600	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
42	chr1:209958200-209958600	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
43	chr1:209958200-209958600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr1:209958200-209958600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr1:209958200-209958600	Flanking Active TSS	Primary B cells from cord blood	blood
46	chr1:209958200-209958600	Flanking Active TSS	Primary T cells from cord blood	blood
47	chr1:209958200-209958600	Flanking Active TSS	Primary hematopoietic stem cells	blood
48	chr1:209958200-209958600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
49	chr1:209958200-209958600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
50	chr1:209958200-209958600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood

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