Variant report

Variant	rs11678190
Chromosome Location	chr2:187560308-187560309
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	WRNIP1	chr2:187559907-187560410	GM12878	blood:	n/a	n/a
2	MYC	chr2:187560136-187560439	MCF10A-Er-Src	breast:	n/a	n/a
3	PBX3	chr2:187559985-187560625	SK-N-SH	brain:	n/a	chr2:187560580-187560589 chr2:187560578-187560589
4	MAX	chr2:187560181-187560321	GM12878	blood:	n/a	n/a
5	POLR2A	chr2:187560124-187560513	SK-N-SH	brain:	n/a	n/a
6	KAP1	chr2:187559940-187560541	U2OS	brain:	n/a	n/a
7	EP300	chr2:187560234-187560558	GM12878	blood:	n/a	chr2:187560319-187560326
8	STAT3	chr2:187560288-187560468	MCF10A-Er-Src	breast:	n/a	n/a
9	MAFK	chr2:187559906-187560448	IMR90	lung:	n/a	n/a
10	GATA2	chr2:187559879-187560497	SH-SY5Y	brain:	n/a	n/a
11	MAZ	chr2:187560231-187560445	GM12878	blood:	n/a	n/a
12	FOS	chr2:187560249-187560417	MCF10A-Er-Src	breast:	n/a	n/a
13	FOS	chr2:187560178-187560496	MCF10A-Er-Src	breast:	n/a	n/a
14	REST	chr2:187558107-187560631	H1-neurons	neurons:	n/a	chr2:187558532-187558539
15	PBX3	chr2:187560038-187560542	SK-N-SH	brain:	n/a	n/a
16	MAX	chr2:187559979-187560566	SK-N-SH	brain:	n/a	n/a
17	POLR2A	chr2:187560194-187560495	H1-neurons	neurons:	n/a	n/a
18	TCF12	chr2:187559919-187560595	SK-N-SH	brain:	n/a	chr2:187560305-187560312
19	RFX5	chr2:187560176-187560343	GM12878	blood:	n/a	n/a
20	E2F4	chr2:187560187-187560364	MCF10A-Er-Src	breast:	n/a	chr2:187560233-187560242
21	FOS	chr2:187560115-187560469	MCF10A-Er-Src	breast:	n/a	n/a
22	EP300	chr2:187560190-187560527	SK-N-SH_RA	brain:	n/a	chr2:187560319-187560326
23	MYC	chr2:187559931-187560373	MCF10A-Er-Src	breast:	n/a	n/a
24	GATA3	chr2:187559850-187560324	SH-SY5Y	brain:	n/a	n/a
25	BHLHE40	chr2:187560027-187560575	GM12878	blood:	n/a	n/a
26	MXI1	chr2:187557978-187560961	SK-N-SH	brain:	n/a	n/a
27	MXI1	chr2:187560287-187560548	GM12878	blood:	n/a	n/a
28	CHD2	chr2:187560259-187560457	GM12878	blood:	n/a	n/a
29	MAX	chr2:187560121-187560539	SK-N-SH	brain:	n/a	n/a

Variant related genes	Relation type
ENSG00000227227	TF binding region

Extended variants
information (count: 61 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10171481	0.85[CHB][hapmap]
rs10804007	0.85[CHB][hapmap]
rs11683898	0.89[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs11685758	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12151442	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12615659	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12998294	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13001028	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13006483	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.85[JPT][hapmap];0.95[TSI][hapmap];0.85[EUR][1000 genomes]
rs13006571	0.85[CHB][hapmap]
rs13016261	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13026081	0.87[CEU][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs13027560	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13028817	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13030356	1.00[CHB][hapmap];0.94[CHD][hapmap];0.91[GIH][hapmap];0.84[TSI][hapmap];0.87[ASN][1000 genomes]
rs13033579	0.91[EUR][1000 genomes]
rs1448424	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.84[EUR][1000 genomes]
rs17334303	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17334422	1.00[CHB][hapmap];0.85[JPT][hapmap];0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs17406339	1.00[CHB][hapmap];0.85[JPT][hapmap];0.96[ASN][1000 genomes]
rs17750683	0.83[CEU][hapmap];0.81[EUR][1000 genomes]
rs1839121	0.84[EUR][1000 genomes]
rs1839123	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1839124	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1992898	0.85[CHB][hapmap]
rs2084448	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2165656	0.85[CHB][hapmap]
rs2197138	0.85[CHB][hapmap]
rs2197787	0.84[CHB][hapmap]
rs2370693	0.85[CHB][hapmap]
rs2595375	0.85[CHB][hapmap];0.98[GIH][hapmap];0.90[TSI][hapmap]
rs2887827	0.85[CHB][hapmap]
rs34483988	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34521209	0.84[ASN][1000 genomes]
rs34980163	0.83[EUR][1000 genomes]
rs35055112	0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs35251833	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35986780	0.91[EUR][1000 genomes]
rs36117902	0.91[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs3768778	0.85[CHB][hapmap]
rs3768780	0.85[CHB][hapmap]
rs3816386	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3911084	0.85[CHB][hapmap]
rs4233788	0.85[CHB][hapmap]
rs58644770	0.87[ASN][1000 genomes]
rs6717512	1.00[CHB][hapmap];0.82[JPT][hapmap];0.90[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6741369	0.85[CHB][hapmap]
rs6748509	0.84[EUR][1000 genomes]
rs7419327	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7575516	0.84[EUR][1000 genomes]
rs7589470	1.00[CHB][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs7593018	0.85[JPT][hapmap]
rs7596996	0.85[CHB][hapmap]
rs9333287	0.85[CHB][hapmap]
rs9333288	0.85[CHB][hapmap]
rs9333289	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];0.85[JPT][hapmap];0.92[TSI][hapmap];0.80[EUR][1000 genomes]
rs9333290	1.00[CEU][hapmap];0.92[TSI][hapmap];0.85[EUR][1000 genomes]
rs9789682	0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs998972	1.00[CHB][hapmap];0.94[CHD][hapmap];0.91[GIH][hapmap];0.83[MEX][hapmap];0.84[TSI][hapmap];0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757844	chr2:187332780-187580547	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
2	esv2759107	chr2:187332780-187580547	Enhancers Bivalent/Poised TSS Active TSS Genic enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11678190	FAM171B	cis	parietal	SCAN
rs11678190	FAM171B	cis	cerebellum	SCAN

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:187558000-187560400	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr2:187558000-187560400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr2:187558000-187560400	Active TSS	Breast Myoepithelial Primary Cells	Breast
4	chr2:187558000-187560400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr2:187558000-187560600	Active TSS	HUES6 Cell Line	embryonic stem cell
6	chr2:187558000-187563000	Active TSS	Brain Inferior Temporal Lobe	brain
7	chr2:187558200-187560400	Active TSS	H1 Cell Line	embryonic stem cell
8	chr2:187558200-187560400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr2:187558200-187560400	Active TSS	Rectal Smooth Muscle	rectum
10	chr2:187558200-187560600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr2:187558200-187560600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr2:187558200-187560600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr2:187558200-187560600	Active TSS	Brain Substantia Nigra	brain
14	chr2:187558200-187560600	Active TSS	Fetal Kidney	kidney
15	chr2:187558200-187560600	Active TSS	Pancreatic Islets	Pancreatic Islet
16	chr2:187558200-187560800	Active TSS	Brain Hippocampus Middle	brain
17	chr2:187558200-187561200	Active TSS	Brain Angular Gyrus	brain
18	chr2:187558200-187561200	Active TSS	Brain Anterior Caudate	brain
19	chr2:187558400-187560400	Enhancers	Fetal Heart	heart
20	chr2:187558400-187560400	Active TSS	Ovary	ovary
21	chr2:187558400-187560400	Active TSS	Psoas Muscle	Psoas
22	chr2:187558400-187560400	Active TSS	NHDF-Ad	bronchial
23	chr2:187558400-187560600	Active TSS	NHLF	lung
24	chr2:187558600-187560400	Active TSS	Osteobl	bone
25	chr2:187558600-187560600	Active TSS	HUES48 Cell Line	embryonic stem cell
26	chr2:187558600-187561000	Active TSS	Cortex derived primary cultured neurospheres	brain
27	chr2:187558600-187561200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr2:187558600-187561200	Active TSS	Brain Germinal Matrix	brain
29	chr2:187558600-187561200	Active TSS	Fetal Brain Female	brain
30	chr2:187558600-187561400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
31	chr2:187558800-187561200	Active TSS	Fetal Brain Male	brain
32	chr2:187559000-187560400	Flanking Active TSS	Primary hematopoietic stem cells	blood
33	chr2:187559000-187560600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr2:187559000-187560800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr2:187559400-187560400	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
36	chr2:187559400-187560400	Bivalent/Poised TSS	Fetal Intestine Small	intestine
37	chr2:187559400-187560400	Active TSS	Fetal Muscle Trunk	muscle
38	chr2:187559400-187560600	Active TSS	Fetal Muscle Leg	muscle
39	chr2:187559400-187560600	Enhancers	Dnd41	blood
40	chr2:187559400-187560800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
41	chr2:187559600-187560400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr2:187559600-187560400	Bivalent Enhancer	Monocytes-CD14+_RO01746	blood
43	chr2:187559600-187560600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr2:187559600-187561200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
45	chr2:187559800-187560400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
46	chr2:187559800-187560400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr2:187559800-187560400	Flanking Active TSS	Fetal Lung	lung
48	chr2:187559800-187560400	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
49	chr2:187559800-187560400	Flanking Active TSS	HUVEC	blood vessel
50	chr2:187560000-187560400	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell

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