Variant report

Variant	rs6759700
Chromosome Location	chr2:10056858-10056859
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:9940167..9943661-chr2:10053697..10057580,3	MCF-7	breast:
2	chr2:10055984..10058361-chr2:10061943..10063449,2	MCF-7	breast:
3	chr2:10037949..10040040-chr2:10055239..10057291,2	MCF-7	breast:

Extended variants
information (count: 57 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs1022312	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10495576	0.81[CEU][hapmap]
rs1054561	0.84[CEU][hapmap]
rs1054565	0.81[CEU][hapmap]
rs11686239	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11691885	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12185679	0.81[CEU][hapmap]
rs12468764	0.80[CEU][hapmap]
rs12479251	0.81[CEU][hapmap]
rs12614753	0.81[CEU][hapmap]
rs12615461	0.81[CEU][hapmap]
rs12617033	0.81[CEU][hapmap]
rs12621371	0.84[CEU][hapmap]
rs12991584	0.81[CEU][hapmap]
rs12995394	0.84[CEU][hapmap]
rs13002884	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1367385	0.84[CEU][hapmap]
rs16867210	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16867226	0.84[CEU][hapmap]
rs1835426	0.81[CEU][hapmap]
rs1965411	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1971101	0.89[YRI][hapmap];0.83[AFR][1000 genomes]
rs2052948	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2163337	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2241665	0.81[CEU][hapmap]
rs2303921	0.96[YRI][hapmap];0.86[AFR][1000 genomes]
rs2884175	0.80[AMR][1000 genomes]
rs34577787	0.80[CEU][hapmap]
rs35390016	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35466574	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35686192	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs372222	0.81[CEU][hapmap]
rs3815977	0.81[CEU][hapmap]
rs445742	0.81[CEU][hapmap]
rs450085	0.81[CEU][hapmap]
rs4668650	0.81[CEU][hapmap]
rs4668654	0.80[CEU][hapmap]
rs4669490	0.84[CEU][hapmap]
rs4669492	0.84[CEU][hapmap]
rs4669493	0.84[CEU][hapmap]
rs514905	0.81[CEU][hapmap]
rs57046626	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6432041	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6707700	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6707887	0.84[CEU][hapmap];0.81[AMR][1000 genomes]
rs6742427	0.81[CEU][hapmap]
rs6748720	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948591	chr2:9922257-10141191	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
2	nsv873631	chr2:9975557-10059770	Enhancers Genic enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	21 gene(s)	inside rSNPs	diseases
3	esv1843231	chr2:9979766-10141191	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
4	nsv580960	chr2:9993451-10066694	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv1011125	chr2:9996740-10293803	Enhancers Strong transcription Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
6	nsv1011689	chr2:10023891-10293803	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
7	nsv1006533	chr2:10030964-10065624	Enhancers Flanking Active TSS Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv1004743	chr2:10031389-10065624	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	nsv1005938	chr2:10043181-10074384	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	nsv1003855	chr2:10045055-10059844	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6759700	TAF1B	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:9993800-10079600	Weak transcription	Gastric	stomach
2	chr2:10017800-10073000	Weak transcription	Right Ventricle	heart
3	chr2:10026000-10072800	Weak transcription	Stomach Smooth Muscle	stomach
4	chr2:10030400-10077200	Weak transcription	Aorta	Aorta
5	chr2:10030600-10080600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr2:10036000-10065800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr2:10036600-10076200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr2:10036800-10073000	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr2:10037200-10080400	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr2:10037800-10075600	Weak transcription	Brain Cingulate Gyrus	brain
11	chr2:10038600-10079800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr2:10038600-10081400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr2:10039000-10058600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr2:10039400-10059400	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr2:10042600-10077000	Weak transcription	Colon Smooth Muscle	Colon
16	chr2:10044200-10065200	Strong transcription	Monocytes-CD14+_RO01746	blood
17	chr2:10045000-10058400	Weak transcription	Psoas Muscle	Psoas
18	chr2:10045800-10079600	Weak transcription	Esophagus	oesophagus
19	chr2:10046000-10075200	Weak transcription	Brain Hippocampus Middle	brain
20	chr2:10047200-10061600	Strong transcription	Primary T cells fromperipheralblood	blood
21	chr2:10047200-10080000	Weak transcription	Colonic Mucosa	Colon
22	chr2:10048600-10058400	Weak transcription	Rectal Smooth Muscle	rectum
23	chr2:10049000-10077400	Weak transcription	Brain Anterior Caudate	brain
24	chr2:10049400-10077200	Weak transcription	Brain Angular Gyrus	brain
25	chr2:10049400-10081000	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr2:10049600-10065200	Strong transcription	Primary monocytes fromperipheralblood	blood
27	chr2:10049600-10081200	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr2:10050200-10061200	Weak transcription	Stomach Mucosa	stomach
29	chr2:10050600-10058000	Strong transcription	HUES64 Cell Line	embryonic stem cell
30	chr2:10050800-10057000	Strong transcription	Dnd41	blood
31	chr2:10050800-10057600	Strong transcription	Fetal Thymus	thymus
32	chr2:10051000-10057000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr2:10051000-10057200	Strong transcription	Primary T helper cells fromperipheralblood	blood
34	chr2:10051000-10057400	Weak transcription	Fetal Heart	heart
35	chr2:10051000-10061200	Strong transcription	HUES48 Cell Line	embryonic stem cell
36	chr2:10051200-10064400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
37	chr2:10051400-10059400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr2:10052400-10058800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
39	chr2:10052800-10076600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr2:10053200-10057800	Weak transcription	Left Ventricle	heart
41	chr2:10053200-10077800	Weak transcription	Liver	Liver
42	chr2:10053800-10060600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
43	chr2:10054600-10057400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr2:10054600-10073400	Weak transcription	Brain Substantia Nigra	brain
45	chr2:10054800-10058400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr2:10054800-10059800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr2:10054800-10063600	Weak transcription	Small Intestine	intestine
48	chr2:10054800-10065000	Weak transcription	Lung	lung
49	chr2:10054800-10066000	Weak transcription	Fetal Brain Male	brain
50	chr2:10054800-10069200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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