Variant report

Variant	rs9941087
Chromosome Location	chr16:72118324-72118325
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	chr16:72116485-72119281	K562	blood:	n/a	n/a
2	CBX3	chr16:72118288-72118762	K562	blood:	n/a	n/a
3	KAP1	chr16:72118177-72118743	K562	blood:	n/a	chr16:72118279-72118287
4	POLR2A	chr16:72118312-72118426	MCF10A-Er-Src	breast:	n/a	n/a
5	POLR2A	chr16:72118286-72118545	K562	blood:	n/a	n/a
6	TRIM28	chr16:72118303-72118748	K562	blood:	n/a	n/a
7	POLR2A	chr16:72118272-72118388	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr16:72117553..72119364-chr16:72127046..72129363,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000260252	TF binding region
ENSG00000140830	Chromatin interaction
ENSG00000140829	Chromatin interaction

Extended variants
information (count: 96 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs1035559	0.80[CEU][hapmap];0.91[GIH][hapmap];0.95[MEX][hapmap]
rs10492813	0.80[CEU][hapmap];0.96[GIH][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10492814	0.80[CEU][hapmap];0.96[GIH][hapmap];0.89[JPT][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1050361	0.83[CEU][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1050362	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.98[TSI][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1050363	0.90[JPT][hapmap]
rs11075922	0.82[ASN][1000 genomes]
rs11862813	0.81[EUR][1000 genomes]
rs11864453	0.80[CEU][hapmap];0.91[GIH][hapmap];0.90[MEX][hapmap]
rs12325142	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.98[TSI][hapmap];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12444701	0.89[ASN][1000 genomes]
rs12445401	0.90[ASN][1000 genomes]
rs12445586	0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12448315	0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12708925	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12708926	0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12708927	0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12708928	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12924413	0.83[CEU][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs12924886	0.88[ASN][1000 genomes]
rs12928732	0.83[ASW][hapmap];0.90[CHB][hapmap];0.89[CHD][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap]
rs13334151	0.95[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap]
rs16973716	0.85[CHB][hapmap];0.81[CHD][hapmap];0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs2000999	0.84[CHB][hapmap];0.94[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs2072141	0.87[CEU][hapmap];0.95[JPT][hapmap]
rs2072142	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.98[TSI][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2074626	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.98[TSI][hapmap];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2074627	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.98[TSI][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2240243	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2241411	0.81[JPT][hapmap]
rs2241412	0.88[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.85[TSI][hapmap];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2287997	0.94[ASN][1000 genomes]
rs2303285	0.80[CEU][hapmap];0.96[GIH][hapmap];0.95[JPT][hapmap];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2550035	0.80[CEU][hapmap];0.96[GIH][hapmap];0.95[JPT][hapmap];0.82[EUR][1000 genomes]
rs2550038	0.80[CEU][hapmap];0.89[JPT][hapmap];0.83[EUR][1000 genomes]
rs2854956	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3213422	0.93[YRI][hapmap]
rs34042070	0.87[ASN][1000 genomes]
rs34714490	0.80[ASN][1000 genomes]
rs35460163	0.80[ASN][1000 genomes]
rs3764311	0.95[JPT][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3764312	0.91[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.87[TSI][hapmap];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3764314	0.80[CEU][hapmap];0.96[GIH][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3794695	0.88[ASN][1000 genomes]
rs3812987	0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.88[ASN][1000 genomes]
rs3852781	0.80[CEU][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3902135	0.83[ASW][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap];0.80[ASN][1000 genomes]
rs4788597	0.93[YRI][hapmap]
rs5472	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6416742	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6499559	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6499560	0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6499561	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6499562	0.85[CHB][hapmap];0.83[CHD][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs6680	0.90[CHB][hapmap];0.94[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7184169	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.89[ASN][1000 genomes]
rs7185407	0.80[CEU][hapmap];0.91[GIH][hapmap];0.95[MEX][hapmap]
rs7186207	0.86[YRI][hapmap]
rs7188058	0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap];0.84[ASN][1000 genomes]
rs7190995	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7191127	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7192730	0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7194397	0.81[ASN][1000 genomes]
rs7197453	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7197869	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7198572	0.83[ASW][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap];0.86[YRI][hapmap];0.80[ASN][1000 genomes]
rs7940	0.81[JPT][hapmap]
rs8044555	0.95[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.80[MKK][hapmap];0.93[YRI][hapmap];0.88[ASN][1000 genomes]
rs8044868	0.85[CHB][hapmap];0.81[CHD][hapmap];0.85[JPT][hapmap]
rs8047377	0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8050238	1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs8051882	0.91[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.82[TSI][hapmap];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8052408	0.85[CHB][hapmap];0.86[CHD][hapmap];0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs8058609	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8059378	0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8059437	0.81[JPT][hapmap]
rs8061282	0.89[ASN][1000 genomes]
rs8061459	0.89[ASN][1000 genomes]
rs8062041	0.95[CEU][hapmap];0.87[CHB][hapmap];0.94[JPT][hapmap];0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs929866	0.86[YRI][hapmap]
rs9925763	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9926156	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9926927	0.80[CEU][hapmap];0.96[GIH][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9928157	0.81[JPT][hapmap]
rs9932951	0.81[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	nsv948468	chr16:71727571-72651914	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats 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	89 gene(s)	inside rSNPs	diseases
2	nsv833273	chr16:71971805-72152854	Weak transcription Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
3	esv2758430	chr16:71976344-72274347	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
4	esv2758654	chr16:71976344-72274347	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
5	nsv428329	chr16:71976344-72274347	Strong transcription Enhancers Weak transcription Flanking Active TSS 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	34 gene(s)	inside rSNPs	diseases
6	nsv1060983	chr16:72074832-72791629	Genic enhancers ZNF genes & repeats Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases
7	nsv534588	chr16:72078262-72287230	ZNF genes & repeats Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
8	nsv1060804	chr16:72078486-72791629	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases
9	nsv978167	chr16:72088322-72118671	Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	n/a
10	esv1808086	chr16:72088669-72128767	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	22 gene(s)	inside rSNPs	n/a
11	esv3343168	chr16:72111500-72128436	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	22 gene(s)	inside rSNPs	n/a

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs9941087	HP	cis	cerebellum	SCAN
rs9941087	DHODH	cis	Artery Tibial	GTEx
rs9941087	HP	cis	parietal	SCAN
rs9941087	NRN1L	cis	parietal	SCAN
rs9941087	DHODH	cis	cerebellum	SCAN
rs9941087	DHODH	cis	Nerve Tibial	GTEx
rs9941087	DHX38	cis	multi-tissue	Pritchard
rs9941087	HPR	cis	cerebellum	SCAN
rs9941087	DHODH	cis	Esophagus Muscularis	GTEx
rs9941087	DHX38	cis	lymphoblastoid	seeQTL
rs9941087	HPR	cis	parietal	SCAN
rs9941087	ENSG00000140829	cis	multi-tissue	Pritchard

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:72090200-72118400	Weak transcription	Lung	lung
2	chr16:72093800-72118400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr16:72093800-72118400	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr16:72102800-72118400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr16:72106600-72126400	Weak transcription	Small Intestine	intestine
6	chr16:72108000-72126400	Weak transcription	Fetal Heart	heart
7	chr16:72108200-72118400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr16:72108200-72118400	Weak transcription	Fetal Brain Female	brain
9	chr16:72108400-72118400	Weak transcription	Brain Anterior Caudate	brain
10	chr16:72108400-72118400	Weak transcription	Fetal Muscle Leg	muscle
11	chr16:72108400-72118400	Weak transcription	Right Ventricle	heart
12	chr16:72108400-72118600	Weak transcription	Colon Smooth Muscle	Colon
13	chr16:72108400-72119000	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr16:72108600-72118400	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr16:72108600-72118400	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr16:72108600-72118400	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr16:72108800-72118400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr16:72108800-72118600	Weak transcription	K562	blood
19	chr16:72108800-72118800	Weak transcription	Gastric	stomach
20	chr16:72109000-72118400	Weak transcription	Right Atrium	heart
21	chr16:72109000-72118600	Weak transcription	Brain Cingulate Gyrus	brain
22	chr16:72109000-72122600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
23	chr16:72109600-72118400	Weak transcription	Aorta	Aorta
24	chr16:72109600-72118400	Weak transcription	Pancreas	Pancrea
25	chr16:72109600-72118600	Weak transcription	Stomach Mucosa	stomach
26	chr16:72110000-72118600	Weak transcription	HSMM	muscle
27	chr16:72110200-72122800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
28	chr16:72110600-72118400	Weak transcription	Primary T helper cells PMA-I stimulated	--
29	chr16:72110800-72118400	Weak transcription	Pancreatic Islets	Pancreatic Islet
30	chr16:72111000-72120000	Weak transcription	NHLF	lung
31	chr16:72111200-72118600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
32	chr16:72111400-72118400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr16:72112000-72118400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
34	chr16:72112000-72118400	Weak transcription	Spleen	Spleen
35	chr16:72112200-72118400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr16:72115600-72118400	Weak transcription	Fetal Intestine Large	intestine
37	chr16:72115800-72118400	Weak transcription	Fetal Brain Male	brain
38	chr16:72116000-72118600	Weak transcription	Fetal Kidney	kidney
39	chr16:72116200-72118600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr16:72116800-72118400	Weak transcription	Rectal Smooth Muscle	rectum
41	chr16:72116800-72118600	Weak transcription	NH-A	brain
42	chr16:72116800-72119000	Weak transcription	Placenta Amnion	Placenta Amnion
43	chr16:72117000-72118600	Weak transcription	Hela-S3	cervix
44	chr16:72117000-72118600	Weak transcription	NHDF-Ad	bronchial
45	chr16:72117000-72119400	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
46	chr16:72117000-72126600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
47	chr16:72117200-72118600	Weak transcription	HUVEC	blood vessel
48	chr16:72117200-72119600	ZNF genes & repeats	Primary hematopoietic stem cells	blood
49	chr16:72117600-72118800	Weak transcription	HUES48 Cell Line	embryonic stem cell
50	chr16:72117800-72118800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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