Variant report

Variant	rs3800387
Chromosome Location	chr6:35186501-35186502
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:35186126..35189088-chr6:35223923..35225540,2	K562	blood:
2	chr6:35177824..35181731-chr6:35185438..35190079,5	K562	blood:
3	chr6:35170890..35173888-chr6:35185679..35187377,2	K562	blood:
4	chr6:35182919..35187135-chr6:35197439..35201271,4	K562	blood:
5	chr6:35185173..35187713-chr6:35194979..35197264,2	K562	blood:
6	chr6:34855917..34858790-chr6:35184012..35186610,2	K562	blood:
7	chr6:35178452..35180834-chr6:35183642..35187997,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000064999	Chromatin interaction

Extended variants
information (count: 134 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:131)

rs_ID	r²[population]
rs10080361	0.94[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs1013907	0.94[ASN][1000 genomes]
rs1034449	1.00[MKK][hapmap]
rs10755687	0.89[CHD][hapmap];0.82[JPT][hapmap]
rs10807150	0.89[CHD][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs10947540	0.94[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs1108709	0.85[ASN][1000 genomes]
rs1194	0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs12173347	1.00[CEU][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12173582	1.00[ASW][hapmap];1.00[CEU][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[AFR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12211765	1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12211943	0.81[ASN][1000 genomes]
rs13214290	0.94[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs1557567	0.89[CHD][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs1557568	0.89[CHD][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs1590381	0.83[ASN][1000 genomes]
rs16872484	0.82[AFR][1000 genomes]
rs1888822	0.83[CHD][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs1888823	0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1888824	0.94[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs1888825	0.94[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs1894650	0.94[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs1894651	0.82[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1894652	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1894653	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1929847	0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1929849	0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs1987673	0.89[CHD][hapmap];0.82[JPT][hapmap];0.85[ASN][1000 genomes]
rs2006184	0.87[ASN][1000 genomes]
rs2018373	0.85[ASN][1000 genomes]
rs2032538	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2057537	1.00[ASW][hapmap];0.90[LWK][hapmap];0.89[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap]
rs2071920	0.89[CHD][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs2183834	0.85[ASN][1000 genomes]
rs2267657	0.89[CHD][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs2267658	0.90[ASN][1000 genomes]
rs2267660	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2267661	0.95[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2267662	0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2267663	0.94[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2267664	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2284195	0.91[ASN][1000 genomes]
rs2296194	1.00[ASW][hapmap];0.82[LWK][hapmap];0.89[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap]
rs2395614	0.81[JPT][hapmap];0.84[ASN][1000 genomes]
rs34156110	0.81[ASN][1000 genomes]
rs3756855	0.82[AFR][1000 genomes]
rs3777744	0.86[CHD][hapmap];0.82[JPT][hapmap]
rs3798342	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3798343	0.91[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];1.00[TSI][hapmap];0.81[ASN][1000 genomes]
rs3800382	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3800383	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3800385	0.94[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs3800386	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][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]
rs3800388	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][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]
rs3800392	0.87[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs3800393	0.84[ASN][1000 genomes]
rs3800396	0.87[ASN][1000 genomes]
rs3800398	0.87[ASN][1000 genomes]
rs3800399	0.88[ASN][1000 genomes]
rs3800400	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4583983	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4711409	0.94[ASN][1000 genomes]
rs4711411	0.94[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs4711413	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4711414	0.92[ASN][1000 genomes]
rs4713841	0.87[ASN][1000 genomes]
rs4713845	0.94[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs4713848	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4713850	0.81[ASN][1000 genomes]
rs58925593	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62403575	0.92[ASN][1000 genomes]
rs6457812	0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs68164647	0.88[ASN][1000 genomes]
rs6902523	0.94[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs6907324	0.92[ASN][1000 genomes]
rs6907573	0.85[ASN][1000 genomes]
rs6907795	0.87[ASN][1000 genomes]
rs6913037	0.94[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs6913941	0.88[ASN][1000 genomes]
rs6916364	0.88[ASN][1000 genomes]
rs6920747	0.92[ASN][1000 genomes]
rs6927730	0.88[ASN][1000 genomes]
rs6928769	0.95[ASN][1000 genomes]
rs6933979	0.80[CHD][hapmap]
rs6938946	0.88[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs6940375	0.80[ASN][1000 genomes]
rs6941471	0.81[ASN][1000 genomes]
rs72909061	0.95[ASN][1000 genomes]
rs7763946	0.93[ASN][1000 genomes]
rs7769906	0.91[ASN][1000 genomes]
rs7772212	0.92[ASN][1000 genomes]
rs8205	0.82[ASN][1000 genomes]
rs914547	0.94[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs9296144	0.94[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs9296150	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9348962	1.00[ASW][hapmap];0.90[LWK][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap]
rs9348974	0.89[EUR][1000 genomes]
rs9357194	1.00[GIH][hapmap];0.89[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap]
rs9366882	0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs9366883	0.94[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs9366885	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9368852	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9368853	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9368854	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][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]
rs9368857	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9368859	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9368860	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9368865	0.89[EUR][1000 genomes]
rs9380491	1.00[CEU][hapmap]
rs9380492	1.00[ASW][hapmap];0.90[LWK][hapmap];0.89[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap]
rs9380498	0.88[ASN][1000 genomes]
rs9380500	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs9380501	0.94[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs9380502	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9380505	0.89[EUR][1000 genomes]
rs9380507	0.89[EUR][1000 genomes]
rs9394283	0.93[ASN][1000 genomes]
rs9394288	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs9394289	0.91[ASN][1000 genomes]
rs9462065	0.82[JPT][hapmap]
rs9462072	1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9469964	0.94[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs9469972	0.89[CHD][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs9469975	0.82[ASN][1000 genomes]
rs9469979	0.91[ASN][1000 genomes]
rs9469982	0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs9469997	0.81[ASN][1000 genomes]
rs965272	0.81[CHB][hapmap];0.81[JPT][hapmap];0.82[ASN][1000 genomes]
rs968828	0.85[ASN][1000 genomes]
rs975496	0.94[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs991145	0.93[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	esv3428128	chr6:35150524-35225843	Bivalent Enhancer Enhancers Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	esv2758047	chr6:35168116-35291002	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
3	esv2759419	chr6:35168116-35291002	Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3800387	TFF1	trans	brain	seeQTL
rs3800387	SCGB2A2	trans	brain	seeQTL
rs3800387	SCGB1D2	trans	brain	seeQTL
rs3800387	GREM1	trans	brain	seeQTL

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:35182400-35209000	Weak transcription	A549	lung
2	chr6:35182600-35186600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr6:35182600-35186600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr6:35182600-35186600	Enhancers	Placenta Amnion	Placenta Amnion
5	chr6:35182600-35198600	Weak transcription	Gastric	stomach
6	chr6:35182800-35186600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
7	chr6:35182800-35188000	Enhancers	Left Ventricle	heart
8	chr6:35183200-35198800	Weak transcription	Ovary	ovary
9	chr6:35183400-35186600	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
10	chr6:35183600-35189000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr6:35184000-35186800	Enhancers	Aorta	Aorta
12	chr6:35184400-35186600	Enhancers	Placenta	Placenta
13	chr6:35184600-35186600	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr6:35184600-35186600	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
15	chr6:35184600-35186800	Bivalent Enhancer	Fetal Muscle Leg	muscle
16	chr6:35184800-35205600	Weak transcription	Fetal Brain Female	brain
17	chr6:35185000-35186600	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
18	chr6:35185200-35187200	Transcr. at gene 5' and 3'	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr6:35185200-35188200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr6:35185400-35186600	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
21	chr6:35185400-35186600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr6:35185400-35186600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr6:35185400-35186600	Enhancers	Fetal Kidney	kidney
24	chr6:35185400-35186600	Genic enhancers	Fetal Stomach	stomach
25	chr6:35185400-35187600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr6:35185400-35198800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr6:35185600-35186600	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
28	chr6:35185600-35186600	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
29	chr6:35185600-35187000	Enhancers	Fetal Lung	lung
30	chr6:35185600-35188200	Transcr. at gene 5' and 3'	Osteobl	bone
31	chr6:35185600-35189200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr6:35185600-35194200	Enhancers	Fetal Heart	heart
33	chr6:35185800-35187400	Enhancers	Right Atrium	heart
34	chr6:35185800-35188400	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr6:35185800-35198400	Weak transcription	Brain Cingulate Gyrus	brain
36	chr6:35186000-35186600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr6:35186000-35186600	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
38	chr6:35186000-35186600	Enhancers	Primary hematopoietic stem cells short term culture	blood
39	chr6:35186000-35186600	Enhancers	Lung	lung
40	chr6:35186000-35187000	Strong transcription	Stomach Smooth Muscle	stomach
41	chr6:35186200-35186600	Enhancers	Muscle Satellite Cultured Cells	--
42	chr6:35186200-35186600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr6:35186200-35186600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
44	chr6:35186200-35186600	Bivalent Enhancer	HUVEC	blood vessel
45	chr6:35186200-35187800	Weak transcription	NH-A	brain
46	chr6:35186200-35188000	Genic enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr6:35186200-35188000	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr6:35186200-35188400	Weak transcription	HSMMtube	muscle
49	chr6:35186200-35202800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr6:35186400-35186600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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