Variant report

Variant	rs891167
Chromosome Location	chr19:42387803-42387804
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	chr19:42386207-42389350	GM12878	blood:	n/a	n/a
2	MAX	chr19:42387440-42387873	H1-hESC	embryonic stem cell:	n/a	chr19:42387582-42387592 chr19:42387730-42387740
3	MXI1	chr19:42387435-42388784	GM12878	blood:	n/a	n/a
4	POLR2A	chr19:42386253-42388845	GM18505	blood:	n/a	n/a
5	POLR2A	chr19:42387713-42388960	PFSK-1	brain:	n/a	n/a
6	POLR2A	chr19:42386977-42387831	ECC-1	luminal epithelium:	n/a	n/a
7	REST	chr19:42387668-42389025	H1-neurons	neurons:	n/a	chr19:42388917-42388926 chr19:42388344-42388351 chr19:42388856-42388869
8	STAT5A	chr19:42386336-42388814	GM12878	blood:	n/a	chr19:42386500-42386512 chr19:42387421-42387433 chr19:42386487-42386499 chr19:42387251-42387258
9	POLR2A	chr19:42387703-42389082	K562	blood:	n/a	n/a
10	CREB1	chr19:42387784-42388719	HepG2	liver:	n/a	n/a
11	TBP	chr19:42387790-42388844	HepG2	liver:	n/a	chr19:42388793-42388804
12	RCOR1	chr19:42387394-42388499	K562	blood:	n/a	n/a
13	POLR2A	chr19:42387210-42388921	GM12891	blood:	n/a	n/a
14	EGR1	chr19:42387608-42387910	K562	blood:	n/a	n/a
15	STAT5A	chr19:42387703-42388636	K562	blood:	n/a	n/a
16	MAX	chr19:42387431-42388018	H1-hESC	embryonic stem cell:	n/a	chr19:42387582-42387592 chr19:42387730-42387740
17	FOXM1	chr19:42387555-42388710	GM12878	blood:	n/a	n/a
18	POU2F2	chr19:42387414-42388713	GM12878	blood:	n/a	chr19:42387443-42387455
19	POLR2A	chr19:42386288-42388867	Raji	blood:	n/a	n/a
20	CHD1	chr19:42387376-42388825	GM12878	blood:	n/a	chr19:42388361-42388371
21	ZNF143	chr19:42387751-42388651	K562	blood:	n/a	n/a
22	POLR2A	chr19:42386508-42388740	GM12878	blood:	n/a	n/a
23	ZNF143	chr19:42387803-42388668	GM12878	blood:	n/a	n/a
24	YY1	chr19:42387581-42387860	K562	blood:	n/a	n/a
25	CREB1	chr19:42386678-42388758	GM12878	blood:	n/a	n/a
26	POLR2A	chr19:42387685-42388650	HCT-116	colon:	n/a	n/a
27	TBL1XR1	chr19:42387765-42388753	GM12878	blood:	n/a	n/a
28	POLR2A	chr19:42387685-42388713	SK-N-MC	brain:	n/a	n/a
29	POLR2A	chr19:42386792-42388879	HUVEC	blood vessel:	n/a	n/a
30	MYC	chr19:42387613-42388569	K562	blood:	n/a	chr19:42387730-42387740
31	USF2	chr19:42387643-42388690	GM12878	blood:	n/a	n/a
32	POU2F2	chr19:42387196-42388881	GM12891	blood:	n/a	chr19:42387443-42387455
33	ATF2	chr19:42387605-42388630	GM12878	blood:	n/a	n/a
34	POLR2A	chr19:42387302-42389287	GM12891	blood:	n/a	n/a
35	ELF1	chr19:42386517-42388805	GM12878	blood:	n/a	chr19:42387031-42387043 chr19:42387439-42387448 chr19:42387250-42387263 chr19:42387267-42387280 chr19:42387435-42387444
36	POLR2A	chr19:42386145-42389436	GM12891	blood:	n/a	n/a
37	ATF3	chr19:42387416-42389035	A549	lung:	n/a	n/a
38	POLR2A	chr19:42386829-42388866	MCF-7	breast:	n/a	n/a
39	BCLAF1	chr19:42386249-42388821	GM12878	blood:	n/a	chr19:42388358-42388371 chr19:42387443-42387452 chr19:42388471-42388484
40	PBX3	chr19:42387570-42388796	A549	lung:	n/a	n/a
41	YY1	chr19:42387477-42387836	GM12892	blood:	n/a	n/a
42	ELF1	chr19:42387677-42388927	HCT-116	colon:	n/a	n/a
43	MAX	chr19:42386632-42388868	A549	lung:	n/a	chr19:42387419-42387429 chr19:42387582-42387592 chr19:42387730-42387740
44	TAF1	chr19:42386843-42388946	A549	lung:	n/a	n/a
45	E2F6	chr19:42387495-42388785	A549	lung:	n/a	chr19:42388472-42388482
46	POLR2A	chr19:42386840-42389018	Hela-S3	cervix:	n/a	n/a
47	TBL1XR1	chr19:42387683-42388610	K562	blood:	n/a	n/a
48	POLR2A	chr19:42387045-42388919	MCF-7	breast:	n/a	n/a
49	MAFK	chr19:42387748-42388583	K562	blood:	n/a	n/a
50	POLR2A	chr19:42386995-42388850	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:42385735..42391033-chr19:42460351..42463651,6	K562	blood:
2	chr19:42386056..42389793-chr19:42407267..42411147,5	MCF-7	breast:
3	chr19:42386135..42388674-chr19:42579222..42581788,5	K562	blood:
4	chr19:42385706..42396512-chr19:42423854..42433641,19	K562	blood:
5	chr19:42385318..42391505-chr19:42458040..42463569,9	MCF-7	breast:
6	chr19:42386808..42388903-chr19:42409471..42412143,2	K562	blood:
7	chr19:42385266..42389164-chr19:42392215..42397025,5	MCF-7	breast:
8	chr19:42382327..42390135-chr19:42429723..42437438,12	MCF-7	breast:
9	chr19:42387685..42389812-chr19:42806888..42808559,2	K562	blood:
10	chr19:42386993..42388717-chr19:42395011..42397502,2	K562	blood:
11	chr19:42387549..42389204-chr19:42401111..42402879,2	MCF-7	breast:
12	chr19:42384855..42393410-chr19:42428364..42439251,22	K562	blood:
13	chr19:42386109..42390387-chr19:42411996..42416642,6	K562	blood:
14	chr19:42385036..42390018-chr19:42460408..42463391,5	K562	blood:
15	chr19:42387018..42388903-chr19:42409279..42410971,2	K562	blood:
16	chr19:42386135..42388460-chr19:42579140..42581462,3	K562	blood:
17	chr19:42387518..42388095-chr9:33024637..33025594,2	Hela-S3	cervix:
18	chr19:42362804..42368897-chr19:42386582..42393421,16	MCF-7	breast:
19	chr1:173836951..173837543-chr19:42387798..42388327,2	Hela-S3	cervix:

Variant related genes	Relation type
ARHGEF1	TF binding region
ENSG00000105372	Chromatin interaction
ENSG00000079462	Chromatin interaction
ENSG00000105404	Chromatin interaction
ENSG00000234741	Chromatin interaction
ENSG00000076928	Chromatin interaction
ENSG00000105732	Chromatin interaction
ENSG00000268041	Chromatin interaction
ENSG00000086061	Chromatin interaction
ENSG00000137074	Chromatin interaction
ENSG00000185278	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10404939	0.83[CHB][hapmap];0.82[JPT][hapmap];0.88[YRI][hapmap]
rs10405900	0.91[ASN][1000 genomes]
rs10408367	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs10414823	0.87[CHB][hapmap]
rs10415452	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10416824	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs10417985	0.85[CEU][hapmap];0.83[CHB][hapmap];0.87[GIH][hapmap];0.91[JPT][hapmap];0.83[MEX][hapmap];0.85[MKK][hapmap];0.85[TSI][hapmap];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10500284	0.83[CHB][hapmap]
rs1075728	0.81[CEU][hapmap]
rs12461099	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12461131	0.82[AMR][1000 genomes]
rs12972552	0.83[EUR][1000 genomes]
rs12976571	0.83[CHB][hapmap];0.82[JPT][hapmap];0.88[YRI][hapmap]
rs12977527	0.81[CEU][hapmap]
rs12979253	0.87[CHB][hapmap]
rs12984383	0.80[CEU][hapmap];0.81[CHB][hapmap];0.91[JPT][hapmap];0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs1366610	0.81[CEU][hapmap];0.83[CHB][hapmap];0.84[GIH][hapmap];0.91[JPT][hapmap];0.85[TSI][hapmap];0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs1428922	0.91[ASN][1000 genomes]
rs1457144	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs1870092	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs1870093	0.80[AMR][1000 genomes]
rs2008798	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs2075749	0.82[AMR][1000 genomes]
rs2075750	0.83[CHB][hapmap];0.84[GIH][hapmap];0.91[JPT][hapmap];0.83[TSI][hapmap];0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2075752	0.85[CEU][hapmap];0.83[CHB][hapmap];0.84[GIH][hapmap];0.91[JPT][hapmap];0.82[MEX][hapmap];0.84[TSI][hapmap];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2075754	0.81[CEU][hapmap];0.83[CHB][hapmap];0.84[GIH][hapmap];0.91[JPT][hapmap];0.85[TSI][hapmap];0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2199829	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs2290695	0.82[CHB][hapmap]
rs2305809	0.83[CHB][hapmap]
rs3786536	0.81[CEU][hapmap];0.83[CHB][hapmap];0.91[JPT][hapmap];0.82[AMR][1000 genomes]
rs3786538	0.81[CEU][hapmap];0.83[CHB][hapmap];0.84[GIH][hapmap];0.91[JPT][hapmap];0.85[TSI][hapmap];0.82[AMR][1000 genomes]
rs3810153	0.96[CEU][hapmap];0.87[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.98[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3922888	0.83[CHB][hapmap];0.88[YRI][hapmap]
rs4803511	0.83[CHB][hapmap];0.88[YRI][hapmap]
rs4803512	0.88[YRI][hapmap]
rs58857981	0.84[AMR][1000 genomes]
rs7250787	0.82[AMR][1000 genomes]
rs7254214	0.85[CEU][hapmap];0.83[CHB][hapmap];0.84[GIH][hapmap];0.91[JPT][hapmap];0.83[MEX][hapmap];0.85[MKK][hapmap];0.85[TSI][hapmap];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7257666	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs7258163	0.81[AMR][1000 genomes]
rs7259596	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7259967	0.83[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs734107	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs73549152	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs8102670	0.82[AMR][1000 genomes]
rs8104958	0.83[CHB][hapmap];0.82[JPT][hapmap];0.88[YRI][hapmap]
rs8106505	0.87[CHB][hapmap]
rs8113283	0.83[CHB][hapmap];0.81[JPT][hapmap]
rs8113641	0.80[CHB][hapmap];0.82[JPT][hapmap]
rs873282	0.81[CEU][hapmap];0.83[CHB][hapmap];0.84[GIH][hapmap];0.91[JPT][hapmap];0.85[TSI][hapmap];0.82[AMR][1000 genomes]
rs882520	0.96[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs899662	0.82[JPT][hapmap]

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	nsv522854	chr19:42120283-42931004	Weak transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
2	nsv1061878	chr19:42325490-42416056	Strong transcription Flanking Active TSS Weak transcription Genic enhancers Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv911776	chr19:42343526-42416056	Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Genic 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	29 gene(s)	inside rSNPs	diseases
4	nsv911777	chr19:42357455-42521108	Bivalent/Poised TSS Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	nsv520239	chr19:42357455-42931004	Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Strong transcription Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
6	nsv911778	chr19:42358362-42416056	Strong transcription Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
7	esv1805469	chr19:42367635-42798851	Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	77 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs891167	SLC1A5	cis	parietal	SCAN
rs891167	LIG1	cis	parietal	SCAN
rs891167	ZNF227	cis	cerebellum	SCAN
rs891167	EHD2	cis	parietal	SCAN
rs891167	RABAC1	Cis_1M	lymphoblastoid	RTeQTL
rs891167	IGFL1	cis	parietal	SCAN
rs891167	EXOC3L2	cis	cerebellum	SCAN
rs891167	PPP5C	cis	parietal	SCAN
rs891167	PVR	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:42386200-42388000	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
2	chr19:42386200-42388000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
3	chr19:42386200-42388600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr19:42386400-42388600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr19:42386400-42388800	Active TSS	Muscle Satellite Cultured Cells	--
6	chr19:42386400-42388800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr19:42386400-42388800	Active TSS	Brain Hippocampus Middle	brain
8	chr19:42386400-42388800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
9	chr19:42386400-42389000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr19:42386400-42389000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr19:42386400-42389000	Active TSS	Thymus	Thymus
12	chr19:42386400-42389200	Active TSS	H9 Cell Line	embryonic stem cell
13	chr19:42386600-42388000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
14	chr19:42386600-42388200	Flanking Active TSS	Primary hematopoietic stem cells	blood
15	chr19:42386600-42388200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr19:42386600-42388600	Active TSS	Right Ventricle	heart
17	chr19:42386600-42388800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr19:42386600-42388800	Active TSS	HSMMtube	muscle
19	chr19:42386600-42388800	Active TSS	NHDF-Ad	bronchial
20	chr19:42386600-42389000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr19:42386600-42389000	Active TSS	Aorta	Aorta
22	chr19:42386600-42389000	Active TSS	Gastric	stomach
23	chr19:42386600-42389000	Active TSS	Left Ventricle	heart
24	chr19:42386600-42389000	Active TSS	Right Atrium	heart
25	chr19:42386600-42389000	Active TSS	GM12878-XiMat	blood
26	chr19:42386600-42389000	Active TSS	HSMM	muscle
27	chr19:42386600-42389000	Active TSS	NHLF	lung
28	chr19:42386600-42389200	Active TSS	Fetal Kidney	kidney
29	chr19:42386800-42388200	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr19:42386800-42388600	Active TSS	Primary B cells from peripheral blood	blood
31	chr19:42386800-42388600	Active TSS	Primary T helper naive cells from peripheral blood	blood
32	chr19:42386800-42388600	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
33	chr19:42386800-42388600	Active TSS	Primary T regulatory cells fromperipheralblood	blood
34	chr19:42386800-42388600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr19:42386800-42388800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr19:42386800-42388800	Active TSS	Primary T killer memory cells from peripheral blood	blood
37	chr19:42386800-42388800	Active TSS	Colon Smooth Muscle	Colon
38	chr19:42386800-42388800	Active TSS	Sigmoid Colon	Sigmoid Colon
39	chr19:42386800-42388800	Active TSS	Small Intestine	intestine
40	chr19:42386800-42388800	Active TSS	Spleen	Spleen
41	chr19:42386800-42388800	Active TSS	Hela-S3	cervix
42	chr19:42386800-42388800	Active TSS	NHEK	skin
43	chr19:42386800-42389000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
44	chr19:42386800-42389000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
45	chr19:42386800-42389000	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
46	chr19:42386800-42389000	Active TSS	Lung	lung
47	chr19:42386800-42389000	Active TSS	Ovary	ovary
48	chr19:42386800-42389000	Active TSS	A549	lung
49	chr19:42386800-42389200	Active TSS	Pancreatic Islets	Pancreatic Islet
50	chr19:42386800-42389400	Transcr. at gene 5' and 3'	Primary T helper naive cells fromperipheralblood	blood

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