Variant report

Variant	rs7804318
Chromosome Location	chr7:97796635-97796636
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:97651077..97652849-chr7:97796480..97798083,2	MCF-7	breast:
2	chr7:97735515..97738382-chr7:97794427..97798053,3	K562	blood:
3	chr7:97734947..97737685-chr7:97796527..97798334,3	K562	blood:
4	chr7:97734652..97738073-chr7:97792918..97796975,9	MCF-7	breast:
5	chr7:97759468..97762062-chr7:97796586..97798629,2	K562	blood:
6	chr7:97780327..97782025-chr7:97795539..97798023,2	K562	blood:

Variant related genes	Relation type
ENSG00000164715	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs11762534	1.00[ASW][hapmap];0.94[MEX][hapmap];0.89[AMR][1000 genomes]
rs11763970	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.95[TSI][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11764933	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11765552	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11767962	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11768309	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12666406	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12670686	0.84[AMR][1000 genomes]
rs12674083	0.84[AMR][1000 genomes]
rs13221758	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17435590	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17435847	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2132276	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34307903	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34320230	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3801294	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6465654	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap];0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6465657	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6465658	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.95[TSI][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6946915	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6958572	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6965016	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6967926	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.89[MEX][hapmap];0.93[MKK][hapmap];0.91[TSI][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6969384	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6977321	0.95[CEU][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7791463	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7808528	0.93[CEU][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs940432	0.85[TSI][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	nsv1031371	chr7:97312452-98070538	Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	esv3500384	chr7:97527787-98015382	Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	36 gene(s)	inside rSNPs	diseases
3	esv3500386	chr7:97527787-98015382	Bivalent Enhancer Flanking Active TSS Strong transcription Enhancers Genic enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	36 gene(s)	inside rSNPs	diseases
4	nsv1017481	chr7:97597641-98041043	Active TSS Weak transcription Flanking Active TSS Genic enhancers Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
5	nsv539031	chr7:97597641-98041043	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
6	nsv1019531	chr7:97653880-98034129	Weak transcription Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
7	nsv539032	chr7:97653880-98034129	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
8	esv1816676	chr7:97676259-97868033	Weak transcription Strong transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	nsv831066	chr7:97726879-97890550	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
10	nsv1033029	chr7:97773232-98017992	Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
11	nsv539033	chr7:97773232-98017992	Genic enhancers Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7804318	BAIAP2L1	cis	cerebellum	SCAN
rs7804318	TSC22D4	cis	cerebellum	SCAN
rs7804318	DKFZP434B0335	cis	multi-tissue	Pritchard

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:97763400-97801000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr7:97763400-97821000	Weak transcription	NHLF	lung
3	chr7:97763600-97814200	Weak transcription	Osteobl	bone
4	chr7:97763600-97815800	Weak transcription	HSMM	muscle
5	chr7:97764000-97806200	Weak transcription	Psoas Muscle	Psoas
6	chr7:97765800-97840800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr7:97766600-97798400	Weak transcription	HSMMtube	muscle
8	chr7:97768800-97807000	Weak transcription	Stomach Mucosa	stomach
9	chr7:97771800-97797800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr7:97772400-97821600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr7:97775600-97803600	Weak transcription	K562	blood
12	chr7:97781800-97808200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr7:97782400-97803600	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr7:97782400-97819000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr7:97782400-97822000	Weak transcription	Fetal Kidney	kidney
16	chr7:97782400-97839800	Weak transcription	Fetal Brain Male	brain
17	chr7:97782600-97807400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr7:97784600-97815000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr7:97785000-97801000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr7:97785000-97804000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
21	chr7:97785200-97818600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
22	chr7:97785400-97804600	Weak transcription	NHDF-Ad	bronchial
23	chr7:97785400-97804800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr7:97785600-97804200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr7:97786400-97800800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
26	chr7:97786800-97800400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr7:97786800-97801200	Weak transcription	Placenta	Placenta
28	chr7:97787200-97799400	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr7:97787400-97800200	Weak transcription	Fetal Muscle Trunk	muscle
30	chr7:97787400-97800800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr7:97787400-97801000	Weak transcription	Fetal Muscle Leg	muscle
32	chr7:97787400-97808200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
33	chr7:97787400-97822000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr7:97787800-97800400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr7:97788200-97800400	Weak transcription	Fetal Thymus	thymus
36	chr7:97788400-97800200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr7:97789000-97800000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr7:97789000-97803800	Weak transcription	Brain Germinal Matrix	brain
39	chr7:97789200-97797600	Weak transcription	Skeletal Muscle Male	skeletal muscle
40	chr7:97789200-97798600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
41	chr7:97789200-97800800	Weak transcription	Aorta	Aorta
42	chr7:97789200-97800800	Weak transcription	Thymus	Thymus
43	chr7:97789200-97801000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr7:97789200-97801000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
45	chr7:97789200-97803600	Weak transcription	H1 Cell Line	embryonic stem cell
46	chr7:97789200-97803600	Weak transcription	Fetal Brain Female	brain
47	chr7:97789200-97829400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
48	chr7:97789400-97798800	Weak transcription	Duodenum Smooth Muscle	Duodenum
49	chr7:97789400-97801000	Weak transcription	Primary T cells fromperipheralblood	blood
50	chr7:97789400-97802200	Weak transcription	Left Ventricle	heart

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