Variant report

Variant	rs8102171
Chromosome Location	chr19:40786523-40786524
allele	A/C
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	ZNF263	chr19:40785485-40787027	HEK293-T-REx	kidney:	n/a	n/a
2	POLR2A	chr19:40786113-40786988	GM12878	blood:	n/a	n/a
3	SPI1	chr19:40785944-40786693	GM12878	blood:	n/a	chr19:40786174-40786187
4	ELF1	chr19:40784800-40786773	GM12878	blood:	n/a	chr19:40785706-40785719
5	POLR2A	chr19:40786505-40786885	MCF-7	breast:	n/a	n/a
6	WRNIP1	chr19:40786244-40786687	GM12878	blood:	n/a	n/a
7	POLR2A	chr19:40786445-40786762	GM12878	blood:	n/a	n/a
8	MXI1	chr19:40786194-40786764	GM12878	blood:	n/a	n/a
9	POLR2A	chr19:40786476-40786795	GM12891	blood:	n/a	n/a
10	REST	chr19:40784619-40787303	PANC-1	pancreas:	n/a	chr19:40785994-40786004 chr19:40785201-40785214 chr19:40787050-40787063 chr19:40786402-40786415 chr19:40784931-40784941 chr19:40787050-40787063
11	POLR2A	chr19:40786437-40787235	GM12891	blood:	n/a	n/a
12	SPI1	chr19:40786090-40786570	HL-60	blood:	n/a	chr19:40786174-40786187
13	POLR2A	chr19:40786204-40786990	GM12878	blood:	n/a	n/a
14	POLR2A	chr19:40786342-40787160	K562	blood:	n/a	n/a
15	POLR2A	chr19:40785942-40786935	SK-N-MC	brain:	n/a	n/a
16	POLR2A	chr19:40781762-40793937	PANC-1	pancreas:	n/a	n/a
17	POLR2A	chr19:40786135-40787062	HepG2	liver:	n/a	n/a
18	POLR2A	chr19:40786443-40786546	HepG2	liver:	n/a	n/a
19	POLR2A	chr19:40786514-40786714	MCF-7	breast:	n/a	n/a
20	NFATC1	chr19:40786016-40786656	GM12878	blood:	n/a	n/a
21	SPI1	chr19:40786116-40786529	GM12891	blood:	n/a	chr19:40786174-40786187
22	POLR2A	chr19:40786046-40786986	GM12892	blood:	n/a	n/a
23	POLR2A	chr19:40785547-40787214	K562	blood:	n/a	n/a
24	POLR2A	chr19:40785969-40786948	GM12891	blood:	n/a	n/a
25	POLR2A	chr19:40785526-40787211	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:40731324..40733318-chr19:40786434..40789035,2	MCF-7	breast:
2	chr19:40768260..40771807-chr19:40783478..40786593,4	K562	blood:
3	chr19:40776468..40779839-chr19:40784717..40787633,5	MCF-7	breast:

Variant related genes	Relation type
AKT2	TF binding region
ENSG00000105221	Chromatin interaction
ENSG00000105219	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10402740	0.81[JPT][hapmap];0.87[MEX][hapmap]
rs10405207	0.87[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs1129156	0.82[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.94[MEX][hapmap]
rs11668242	0.86[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.94[TSI][hapmap];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11880261	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12609706	0.84[ASN][1000 genomes]
rs12974529	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12981110	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2304184	0.82[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.94[MEX][hapmap]
rs2304189	0.89[CHB][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs339526	0.90[CHB][hapmap];0.85[JPT][hapmap];0.93[MEX][hapmap]
rs3730050	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3730051	0.82[CEU][hapmap];0.80[CHB][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.87[TSI][hapmap];0.80[ASN][1000 genomes]
rs4239504	0.82[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.94[MEX][hapmap]
rs4239506	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4257318	0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.94[TSI][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4277441	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4332845	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4337402	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4490099	0.95[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4499338	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4558508	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4802070	0.82[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.94[MEX][hapmap]
rs4802071	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4802073	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4802074	0.82[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.81[MEX][hapmap];0.81[TSI][hapmap]
rs4803320	0.82[CEU][hapmap];0.89[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6508936	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7248338	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7249146	0.91[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.91[TSI][hapmap];0.86[ASN][1000 genomes]
rs7250897	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.87[MKK][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7255581	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7257972	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7260106	0.84[ASN][1000 genomes]
rs7260517	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs748236	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7508604	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8100018	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs8104727	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8110888	0.91[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.91[TSI][hapmap];0.84[ASN][1000 genomes]
rs969531	0.95[CEU][hapmap];0.89[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9749283	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1826663	chr19:40529943-41023601	Enhancers Strong transcription Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
2	esv2758499	chr19:40612420-40839520	Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	esv2758761	chr19:40612420-40839520	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
4	nsv911699	chr19:40691632-40816530	Flanking Active TSS Active TSS Strong transcription Weak transcription Genic enhancers Enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
5	esv1833489	chr19:40722123-40923908	Enhancers Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
6	nsv1057052	chr19:40776128-40789766	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases
7	esv1797453	chr19:40780963-40786797	Genic enhancers Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Strong transcription	TF binding region Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
8	esv1005660	chr19:40784738-40790835	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs8102171	TMEM91	cis	parietal	SCAN
rs8102171	IGFL4	cis	parietal	SCAN
rs8102171	FLJ36888	cis	multi-tissue	Pritchard
rs8102171	ERCC1	cis	parietal	SCAN
rs8102171	C19orf47	cis	multi-tissue	Pritchard
rs8102171	ZNF221	cis	parietal	SCAN
rs8102171	C19orf47	cis	lymphoblastoid	seeQTL
rs8102171	SYMPK	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:40766200-40788600	Weak transcription	HSMMtube	muscle
2	chr19:40770000-40789600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr19:40770000-40789600	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr19:40770200-40789600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr19:40770200-40790200	Weak transcription	Aorta	Aorta
6	chr19:40771400-40789400	Weak transcription	HUVEC	blood vessel
7	chr19:40776000-40787400	Weak transcription	A549	lung
8	chr19:40778800-40787600	Weak transcription	Hela-S3	cervix
9	chr19:40779000-40786800	Weak transcription	Dnd41	blood
10	chr19:40779400-40789600	Enhancers	Left Ventricle	heart
11	chr19:40779800-40789800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
12	chr19:40781000-40787800	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr19:40781400-40788000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr19:40781400-40788000	Weak transcription	Primary neutrophils fromperipheralblood	blood
15	chr19:40781600-40787400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr19:40782200-40789400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr19:40782800-40786800	Enhancers	Primary T cells fromperipheralblood	blood
18	chr19:40783000-40788200	Enhancers	Pancreas	Pancrea
19	chr19:40783000-40789600	Enhancers	Primary T killer memory cells from peripheral blood	blood
20	chr19:40783200-40787000	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
21	chr19:40783200-40787400	Enhancers	Fetal Intestine Large	intestine
22	chr19:40783200-40787600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
23	chr19:40783200-40788200	Enhancers	Primary T helper cells fromperipheralblood	blood
24	chr19:40783200-40789200	Enhancers	Brain Cingulate Gyrus	brain
25	chr19:40783400-40786600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr19:40783400-40787400	Enhancers	Lung	lung
27	chr19:40783400-40788000	Enhancers	Brain Anterior Caudate	brain
28	chr19:40783400-40788400	Enhancers	Brain Substantia Nigra	brain
29	chr19:40783400-40790000	Enhancers	Right Atrium	heart
30	chr19:40783600-40787000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr19:40783600-40787000	Enhancers	Primary T helper naive cells from peripheral blood	blood
32	chr19:40783600-40787200	Enhancers	Placenta	Placenta
33	chr19:40783600-40787400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr19:40783600-40787400	Enhancers	Fetal Heart	heart
35	chr19:40783600-40788000	Enhancers	Brain Angular Gyrus	brain
36	chr19:40783800-40787200	Enhancers	Placenta Amnion	Placenta Amnion
37	chr19:40783800-40787600	Enhancers	Primary B cells from peripheral blood	blood
38	chr19:40783800-40788000	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr19:40783800-40790600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr19:40784000-40786800	Genic enhancers	Cortex derived primary cultured neurospheres	brain
41	chr19:40784000-40787000	Enhancers	Primary hematopoietic stem cells	blood
42	chr19:40784000-40787000	Enhancers	Spleen	Spleen
43	chr19:40784000-40787800	Enhancers	Sigmoid Colon	Sigmoid Colon
44	chr19:40784200-40787000	Flanking Active TSS	Stomach Smooth Muscle	stomach
45	chr19:40784200-40787600	Enhancers	Primary B cells from cord blood	blood
46	chr19:40784200-40788000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
47	chr19:40784200-40788200	Enhancers	Psoas Muscle	Psoas
48	chr19:40784400-40786800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr19:40784400-40786800	Enhancers	Muscle Satellite Cultured Cells	--
50	chr19:40784400-40787000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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