Variant report

Variant	rs1538972
Chromosome Location	chr1:161676557-161676558
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	GATA3	chr1:161675907-161676881	SK-N-SH	brain:	n/a	chr1:161676272-161676285 chr1:161676270-161676281 chr1:161676535-161676542 chr1:161676334-161676341
2	FOSL2	chr1:161676143-161676871	SK-N-SH	brain:	n/a	n/a
3	RUNX3	chr1:161675271-161677304	GM12878	blood:	n/a	n/a
4	MTA3	chr1:161675888-161677287	GM12878	blood:	n/a	n/a
5	POLR2A	chr1:161676532-161677323	GM12878	blood:	n/a	n/a
6	PML	chr1:161676308-161677223	GM12878	blood:	n/a	n/a
7	POLR2A	chr1:161675835-161676863	U87	brain:	n/a	n/a
8	RUNX3	chr1:161675286-161677289	GM12878	blood:	n/a	n/a
9	STAT3	chr1:161676418-161676656	MCF10A-Er-Src	breast:	n/a	n/a
10	ELF1	chr1:161676366-161677240	GM12878	blood:	n/a	chr1:161676975-161676986 chr1:161676369-161676380
11	JUN	chr1:161676267-161676956	K562	blood:	n/a	n/a
12	EP300	chr1:161676290-161677140	K562	blood:	n/a	chr1:161676971-161676985 chr1:161676975-161676984
13	POU2F2	chr1:161676219-161677315	GM12878	blood:	n/a	chr1:161676486-161676496 chr1:161676486-161676498 chr1:161676477-161676495 chr1:161676475-161676497 chr1:161676482-161676489 chr1:161676481-161676490 chr1:161676778-161676791 chr1:161677144-161677158 chr1:161676481-161676492 chr1:161676482-161676500 chr1:161676488-161676495 chr1:161676485-161676496 chr1:161676485-161676498 chr1:161676481-161676491 chr1:161677145-161677153 chr1:161676487-161676496 chr1:161676484-161676499 chr1:161677139-161677160 chr1:161676478-161676493 chr1:161677144-161677155
14	POLR2A	chr1:161676318-161677246	GM15510	blood:	n/a	n/a
15	EP300	chr1:161676134-161676788	SK-N-SH	brain:	n/a	n/a
16	ATF3	chr1:161676229-161676963	K562	blood:	n/a	n/a
17	BHLHE40	chr1:161676187-161677219	K562	blood:	n/a	n/a
18	POLR2A	chr1:161676217-161678036	GM12892	blood:	n/a	n/a
19	MEF2A	chr1:161676072-161676934	SK-N-SH	brain:	n/a	chr1:161676446-161676461
20	CEBPD	chr1:161676474-161677252	K562	blood:	n/a	n/a
21	NFYB	chr1:161676394-161677117	GM12878	blood:	n/a	n/a
22	MAZ	chr1:161676298-161677051	K562	blood:	n/a	chr1:161676704-161676713
23	TBL1XR1	chr1:161676293-161677116	K562	blood:	n/a	n/a
24	RCOR1	chr1:161676279-161677221	K562	blood:	n/a	n/a
25	RCOR1	chr1:161676401-161677210	K562	blood:	n/a	n/a
26	SETDB1	chr1:161676092-161676938	U2OS	brain:	n/a	n/a
27	MAFK	chr1:161676428-161677033	K562	blood:	n/a	n/a
28	ATF2	chr1:161675907-161677472	GM12878	blood:	n/a	n/a
29	JUN	chr1:161676271-161676665	K562	blood:	n/a	n/a
30	POLR2A	chr1:161676359-161677266	GM12892	blood:	n/a	n/a
31	POLR2A	chr1:161675236-161678018	Raji	blood:	n/a	n/a
32	POLR2A	chr1:161676391-161677667	GM12878	blood:	n/a	n/a
33	POLR2A	chr1:161675911-161676739	U87	brain:	n/a	n/a
34	CBX3	chr1:161676521-161677151	K562	blood:	n/a	n/a
35	POLR2A	chr1:161676537-161677055	K562	blood:	n/a	n/a
36	IRF4	chr1:161676470-161677107	GM12878	blood:	n/a	n/a
37	POLR2A	chr1:161676470-161677700	GM12892	blood:	n/a	n/a
38	NR2F2	chr1:161676311-161677260	K562	blood:	n/a	n/a
39	YY1	chr1:161676541-161677025	K562	blood:	n/a	n/a
40	BCL11A	chr1:161676167-161677205	GM12878	blood:	n/a	chr1:161676927-161676936
41	KAP1	chr1:161676020-161676966	U2OS	brain:	n/a	n/a
42	MEF2A	chr1:161676006-161677360	GM12878	blood:	n/a	chr1:161676446-161676461
43	IRF4	chr1:161676210-161677313	GM12878	blood:	n/a	n/a
44	JUN	chr1:161676257-161676988	K562	blood:	n/a	n/a
45	YY1	chr1:161676537-161677222	GM12878	blood:	n/a	n/a
46	RELA	chr1:161676014-161677202	GM10847	blood:	n/a	n/a
47	STAT5A	chr1:161676130-161677259	GM12878	blood:	n/a	chr1:161676414-161676421
48	JUND	chr1:161676208-161677129	K562	blood:	n/a	n/a
49	RELA	chr1:161676151-161677242	GM19099	blood:	n/a	n/a
50	POLR2A	chr1:161676433-161677285	GM12891	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:161667779..161671071-chr1:161673847..161676940,3	K562	blood:
2	chr1:161667456..161669424-chr1:161676316..161679255,2	MCF-7	breast:

Variant related genes	Relation type
FCRLA	TF binding region
ENSG00000199595	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs1891018	0.89[CEU][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes]
rs6427622	0.89[CEU][hapmap];0.91[EUR][1000 genomes]
rs7523762	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs7535647	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2756866	chr1:161344255-161681552	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	62 gene(s)	inside rSNPs	diseases
2	esv2758972	chr1:161344255-161681552	Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	62 gene(s)	inside rSNPs	diseases
3	nsv428257	chr1:161406315-161868263	Bivalent/Poised TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
4	esv2755678	chr1:161463498-161678377	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	esv33393	chr1:161478681-162080327	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
6	esv1822760	chr1:161480943-161687379	Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Genic enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
7	esv1817508	chr1:161483404-161678548	Weak transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
8	esv2753408	chr1:161514302-161676557	Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
9	nsv429825	chr1:161514302-161676557	Active TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
10	nsv464184	chr1:161646807-161885352	Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
11	nsv548075	chr1:161646807-161885352	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs1538972	PMF1	cis	cerebellum	SCAN
rs1538972	NDUFS2	cis	parietal	SCAN
rs1538972	ATF6	Cis_1M	lymphoblastoid	RTeQTL
rs1538972	OR6N1	cis	parietal	SCAN
rs1538972	FCRLA	Cis_1M	lymphoblastoid	RTeQTL
rs1538972	CD1E	cis	cerebellum	SCAN
rs1538972	PVRL4	cis	cerebellum	SCAN
rs1538972	FCRLM2	cis	multi-tissue	Pritchard

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:161674800-161676600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr1:161675400-161676600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr1:161675400-161676800	Flanking Active TSS	GM12878-XiMat	blood
4	chr1:161675400-161677000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr1:161675400-161677600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr1:161675400-161677600	Enhancers	HMEC	breast
7	chr1:161675400-161677600	Enhancers	HSMM	muscle
8	chr1:161675400-161677600	Enhancers	NHLF	lung
9	chr1:161675400-161678200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr1:161675400-161678400	Enhancers	NHDF-Ad	bronchial
11	chr1:161675800-161677000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr1:161675800-161677200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr1:161675800-161677200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr1:161675800-161677400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr1:161675800-161680600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
16	chr1:161676000-161676600	Enhancers	Brain Substantia Nigra	brain
17	chr1:161676000-161676600	Enhancers	HSMMtube	muscle
18	chr1:161676000-161676800	Enhancers	Right Atrium	heart
19	chr1:161676000-161676800	Enhancers	Hela-S3	cervix
20	chr1:161676000-161677200	Enhancers	Brain Angular Gyrus	brain
21	chr1:161676000-161677200	Enhancers	Brain Anterior Caudate	brain
22	chr1:161676000-161677200	Enhancers	Brain Hippocampus Middle	brain
23	chr1:161676000-161677200	Enhancers	Fetal Muscle Leg	muscle
24	chr1:161676000-161677200	Enhancers	Skeletal Muscle Male	skeletal muscle
25	chr1:161676000-161677200	Enhancers	NHEK	skin
26	chr1:161676000-161677400	Enhancers	Brain Cingulate Gyrus	brain
27	chr1:161676000-161677600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr1:161676000-161677600	Enhancers	Left Ventricle	heart
29	chr1:161676000-161677600	Enhancers	K562	blood
30	chr1:161676000-161677800	Enhancers	Skeletal Muscle Female	skeletal muscle
31	chr1:161676000-161679800	Flanking Active TSS	Primary B cells from cord blood	blood
32	chr1:161676200-161676800	Enhancers	Adipose Nuclei	Adipose
33	chr1:161676200-161677000	Enhancers	Brain Inferior Temporal Lobe	brain
34	chr1:161676200-161677000	Bivalent Enhancer	Fetal Heart	heart
35	chr1:161676200-161677200	Enhancers	Psoas Muscle	Psoas
36	chr1:161676200-161692000	Weak transcription	Spleen	Spleen
37	chr1:161676400-161676600	Enhancers	Muscle Satellite Cultured Cells	--
38	chr1:161676400-161676600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr1:161676400-161676600	Enhancers	HepG2	liver
40	chr1:161676400-161676600	Enhancers	NH-A	brain
41	chr1:161676400-161676600	Enhancers	Osteobl	bone
42	chr1:161676400-161677000	Flanking Active TSS	Primary B cells from peripheral blood	blood
43	chr1:161676400-161677400	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
44	chr1:161676400-161677400	Bivalent Enhancer	Monocytes-CD14+_RO01746	blood
45	chr1:161676400-161677600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin

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