Variant report

Variant	rs24137
Chromosome Location	chr19:40595917-40595918
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	HCFC1	chr19:40595389-40597742	Hela-S3	cervix:	n/a	n/a
2	MXI1	chr19:40595191-40597631	SK-N-SH	brain:	n/a	n/a
3	POLR2A	chr19:40595305-40596138	HepG2	liver:	n/a	n/a
4	BCL3	chr19:40595876-40597326	A549	lung:	n/a	chr19:40596837-40596846
5	TCF12	chr19:40595852-40597395	A549	lung:	n/a	n/a
6	MAX	chr19:40595652-40597294	A549	lung:	n/a	chr19:40597013-40597022
7	SIN3AK20	chr19:40595272-40597271	PANC-1	pancreas:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:40560174..40562165-chr19:40594393..40596020,2	MCF-7	breast:
2	chr19:40501950..40503610-chr19:40595158..40598072,2	K562	blood:

Variant related genes	Relation type
ENSG00000269296	TF binding region
ENSG00000128000	Chromatin interaction
ENSG00000187187	Chromatin interaction

Extended variants
information (count: 161 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:158)

rs_ID	r²[population]
rs1007628	1.00[CEU][hapmap];0.85[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10401980	0.89[ASN][1000 genomes]
rs10406738	0.86[JPT][hapmap]
rs1327185	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1327187	0.94[ASN][1000 genomes]
rs1327188	0.99[ASN][1000 genomes]
rs1327189	0.98[ASN][1000 genomes]
rs1327190	0.98[ASN][1000 genomes]
rs1327191	0.98[ASN][1000 genomes]
rs1327192	0.98[ASN][1000 genomes]
rs1327193	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs163213	0.82[JPT][hapmap]
rs16973950	0.83[CHB][hapmap];0.84[JPT][hapmap]
rs16974093	0.90[ASN][1000 genomes]
rs170900	0.86[JPT][hapmap]
rs170901	1.00[CEU][hapmap];0.86[JPT][hapmap];0.96[EUR][1000 genomes]
rs173061	0.86[JPT][hapmap]
rs17796901	0.85[JPT][hapmap]
rs17797100	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs183504	0.85[JPT][hapmap]
rs1854098	1.00[ASN][1000 genomes]
rs186815	0.86[JPT][hapmap]
rs1926931	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1926932	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1926933	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1926934	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1998931	0.98[ASN][1000 genomes]
rs2111543	0.86[JPT][hapmap]
rs2111544	0.86[JPT][hapmap]
rs2231737	0.86[JPT][hapmap]
rs234301	0.86[JPT][hapmap]
rs234302	0.86[JPT][hapmap]
rs234304	0.86[JPT][hapmap]
rs234309	0.85[JPT][hapmap]
rs234318	0.86[JPT][hapmap]
rs234323	0.86[JPT][hapmap]
rs234324	0.85[JPT][hapmap]
rs234325	0.85[JPT][hapmap]
rs234340	0.88[JPT][hapmap]
rs234341	0.85[JPT][hapmap]
rs234352	0.86[JPT][hapmap]
rs234353	0.85[JPT][hapmap]
rs234355	0.85[JPT][hapmap]
rs234361	0.86[JPT][hapmap]
rs234370	0.85[JPT][hapmap]
rs234374	0.86[JPT][hapmap]
rs24135	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs24136	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2569639	0.98[ASN][1000 genomes]
rs2569640	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2569641	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2569642	0.98[ASN][1000 genomes]
rs2569643	1.00[ASN][1000 genomes]
rs2569644	1.00[ASN][1000 genomes]
rs2569645	1.00[ASN][1000 genomes]
rs2569648	1.00[ASN][1000 genomes]
rs2569649	1.00[ASN][1000 genomes]
rs2569650	0.93[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2569651	0.94[ASN][1000 genomes]
rs2767592	1.00[ASN][1000 genomes]
rs2767593	1.00[ASN][1000 genomes]
rs2767594	0.99[ASN][1000 genomes]
rs2767595	1.00[ASN][1000 genomes]
rs2767596	1.00[ASN][1000 genomes]
rs2767597	1.00[ASN][1000 genomes]
rs2767598	1.00[ASN][1000 genomes]
rs2767601	0.96[ASN][1000 genomes]
rs2767603	0.98[ASN][1000 genomes]
rs2767604	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2767605	1.00[ASN][1000 genomes]
rs2767606	1.00[ASN][1000 genomes]
rs2767607	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2767608	1.00[ASN][1000 genomes]
rs2767609	1.00[ASN][1000 genomes]
rs2819955	1.00[ASN][1000 genomes]
rs2819956	0.85[JPT][hapmap]
rs2819958	0.98[ASN][1000 genomes]
rs28629274	0.90[ASN][1000 genomes]
rs28890790	0.91[ASN][1000 genomes]
rs2915972	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2970102	1.00[ASN][1000 genomes]
rs2986595	0.85[ASN][1000 genomes]
rs337779	0.86[JPT][hapmap]
rs337780	0.88[JPT][hapmap]
rs337784	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs337785	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs337786	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs337787	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs337788	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs337789	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs337790	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs337791	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs337792	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs337793	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs337794	1.00[CHB][hapmap];0.82[JPT][hapmap];1.00[ASN][1000 genomes]
rs337799	0.85[JPT][hapmap]
rs371500	0.85[JPT][hapmap]
rs387202	0.86[JPT][hapmap]
rs392958	1.00[CEU][hapmap];0.85[JPT][hapmap];0.96[EUR][1000 genomes]
rs421533	0.85[JPT][hapmap]
rs426950	0.85[JPT][hapmap]
rs4577216	1.00[CEU][hapmap];0.85[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs57880771	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs57900299	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs58003479	0.90[ASN][1000 genomes]
rs58210425	0.80[ASN][1000 genomes]
rs58284735	0.80[ASN][1000 genomes]
rs58395013	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs58440570	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs58899236	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58941665	0.80[ASN][1000 genomes]
rs59502139	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs59925663	0.88[EUR][1000 genomes]
rs60449727	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7247527	0.85[JPT][hapmap]
rs7257747	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7258202	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7258506	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7258627	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7258778	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7258974	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7259855	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7260378	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73547676	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73547677	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73547696	0.80[ASN][1000 genomes]
rs73547702	0.80[ASN][1000 genomes]
rs73549804	0.80[ASN][1000 genomes]
rs73549810	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73549811	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73549820	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73549821	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73549825	0.85[ASN][1000 genomes]
rs73549826	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73549829	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73549833	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73549835	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73549836	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73549877	0.99[ASN][1000 genomes]
rs73551642	0.98[ASN][1000 genomes]
rs73551661	0.96[ASN][1000 genomes]
rs73551662	0.96[ASN][1000 genomes]
rs73551663	0.96[ASN][1000 genomes]
rs73551668	0.96[ASN][1000 genomes]
rs73551674	0.96[ASN][1000 genomes]
rs73551675	0.96[ASN][1000 genomes]
rs73551681	0.96[ASN][1000 genomes]
rs73551683	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73551685	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73551687	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73551688	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73551689	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73551691	0.96[ASN][1000 genomes]
rs73551695	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73553603	0.84[ASN][1000 genomes]
rs8103294	0.91[ASN][1000 genomes]
rs8105066	0.85[JPT][hapmap]
rs8106032	1.00[JPT][hapmap];0.91[YRI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv917321	chr19:40403192-40694875	Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	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
3	nsv2488	chr19:40593818-40631406	Active TSS Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs24137	FCGBP	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:40583200-40596000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr19:40591200-40596200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr19:40591200-40596200	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr19:40593600-40596000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
5	chr19:40594800-40596200	Enhancers	Spleen	Spleen
6	chr19:40594800-40596200	Flanking Active TSS	Dnd41	blood
7	chr19:40595200-40596000	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
8	chr19:40595200-40596000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr19:40595200-40596000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
10	chr19:40595200-40596000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr19:40595200-40596000	Flanking Active TSS	Fetal Brain Female	brain
12	chr19:40595200-40596000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
13	chr19:40595200-40596200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr19:40595200-40596200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr19:40595200-40596200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr19:40595200-40596200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
17	chr19:40595200-40596200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
18	chr19:40595200-40597400	Active TSS	ES-I3 Cell Line	embryonic stem cell
19	chr19:40595200-40597400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr19:40595400-40596000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr19:40595400-40596000	Flanking Active TSS	Brain Anterior Caudate	brain
22	chr19:40595400-40596000	Flanking Active TSS	Brain Hippocampus Middle	brain
23	chr19:40595400-40596000	Flanking Active TSS	Colon Smooth Muscle	Colon
24	chr19:40595400-40596000	Flanking Active TSS	Fetal Brain Male	brain
25	chr19:40595400-40596000	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
26	chr19:40595400-40596000	Enhancers	Placenta	Placenta
27	chr19:40595400-40596000	Enhancers	Left Ventricle	heart
28	chr19:40595400-40596000	Enhancers	Lung	lung
29	chr19:40595400-40596000	Enhancers	Pancreas	Pancrea
30	chr19:40595400-40596000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
31	chr19:40595400-40596000	Enhancers	Small Intestine	intestine
32	chr19:40595400-40596200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
33	chr19:40595400-40596200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
34	chr19:40595400-40596200	Flanking Active TSS	Brain Cingulate Gyrus	brain
35	chr19:40595400-40596200	Flanking Active TSS	Brain Substantia Nigra	brain
36	chr19:40595400-40596200	Flanking Active TSS	Fetal Lung	lung
37	chr19:40595400-40596200	Flanking Active TSS	Hela-S3	cervix
38	chr19:40595400-40596200	Flanking Active TSS	HMEC	breast
39	chr19:40595400-40596200	Flanking Active TSS	HSMMtube	muscle
40	chr19:40595400-40596400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
41	chr19:40595400-40596400	Flanking Active TSS	Liver	Liver
42	chr19:40595400-40596400	Flanking Active TSS	NHEK	skin
43	chr19:40595400-40596400	Flanking Active TSS	NHLF	lung
44	chr19:40595400-40596600	Flanking Active TSS	Primary B cells from cord blood	blood
45	chr19:40595400-40596600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
46	chr19:40595400-40596600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr19:40595400-40596600	Flanking Active TSS	Adipose Nuclei	Adipose
48	chr19:40595400-40597000	Active TSS	HUES64 Cell Line	embryonic stem cell
49	chr19:40595400-40597400	Active TSS	H1 Cell Line	embryonic stem cell
50	chr19:40595400-40597400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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