Variant report

Variant	rs12577960
Chromosome Location	chr11:9868141-9868142
allele	C/T
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	GATA3	chr11:9868044-9868354	MCF-7	breast:	n/a	chr11:9868185-9868193
2	FOXA1	chr11:9867980-9868257	T-47D	breast:	n/a	n/a
3	GATA3	chr11:9867924-9868371	T-47D	breast:	n/a	chr11:9868185-9868193
4	GATA3	chr11:9868016-9868445	MCF-7	breast:	n/a	chr11:9868185-9868193
5	GATA3	chr11:9867984-9868371	T-47D	breast:	n/a	chr11:9868185-9868193
6	FOXA1	chr11:9868021-9868202	T-47D	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:9844266..9846481-chr11:9866662..9869256,2	MCF-7	breast:

Variant related genes	Relation type
RNU7-28P	TF binding region

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10770068	0.85[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs10840311	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs11601110	0.81[ASN][1000 genomes]
rs12574461	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12574467	0.92[CHB][hapmap];0.86[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12574474	0.88[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12574508	0.88[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12574765	0.88[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12576762	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12576763	0.87[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12578023	0.87[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12786236	1.00[YRI][hapmap]
rs17268414	0.85[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2403221	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2403222	0.85[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs360118	0.92[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs7108907	0.87[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7937716	0.82[ASN][1000 genomes]
rs7951573	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs958875	1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933855	chr11:9645441-10130519	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking 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	40 gene(s)	inside rSNPs	diseases
2	nsv1053369	chr11:9647837-9876054	Genic enhancers Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv896987	chr11:9759918-9885849	Strong transcription Enhancers Genic enhancers Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
4	esv3384280	chr11:9766350-9911228	Flanking Bivalent TSS/Enh Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
5	esv2762895	chr11:9849511-9954549	Flanking Active TSS Strong transcription Weak transcription Genic enhancers Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:9818600-9881400	Weak transcription	Spleen	Spleen
2	chr11:9826800-9868200	Weak transcription	Aorta	Aorta
3	chr11:9830400-9880400	Weak transcription	Thymus	Thymus
4	chr11:9830800-9880600	Weak transcription	Fetal Brain Male	brain
5	chr11:9833400-9868400	Weak transcription	Fetal Kidney	kidney
6	chr11:9833600-9878800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr11:9834200-9876600	Weak transcription	Brain Germinal Matrix	brain
8	chr11:9834600-9877200	Weak transcription	Right Ventricle	heart
9	chr11:9837600-9885800	Weak transcription	Hela-S3	cervix
10	chr11:9838600-9879800	Weak transcription	Fetal Thymus	thymus
11	chr11:9848200-9877000	Weak transcription	HepG2	liver
12	chr11:9851200-9880000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr11:9851600-9875400	Weak transcription	Stomach Mucosa	stomach
14	chr11:9851600-9880400	Weak transcription	Small Intestine	intestine
15	chr11:9853000-9871600	Weak transcription	Fetal Intestine Small	intestine
16	chr11:9853400-9877400	Weak transcription	Brain Substantia Nigra	brain
17	chr11:9854000-9868400	Weak transcription	Lung	lung
18	chr11:9854000-9877400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr11:9854000-9880600	Weak transcription	Colonic Mucosa	Colon
20	chr11:9856600-9880000	Weak transcription	Fetal Heart	heart
21	chr11:9859000-9872800	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr11:9859600-9871400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr11:9859800-9880200	Strong transcription	Monocytes-CD14+_RO01746	blood
24	chr11:9861000-9868400	Weak transcription	Brain Angular Gyrus	brain
25	chr11:9861400-9868400	Weak transcription	Fetal Brain Female	brain
26	chr11:9861400-9872600	Weak transcription	HUVEC	blood vessel
27	chr11:9861400-9874000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr11:9861400-9875400	Weak transcription	Placenta Amnion	Placenta Amnion
29	chr11:9861400-9877000	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr11:9861400-9877400	Weak transcription	Rectal Smooth Muscle	rectum
31	chr11:9861400-9879600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr11:9861400-9879800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr11:9861400-9879800	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr11:9861400-9880800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
35	chr11:9862400-9868600	Weak transcription	Primary B cells from peripheral blood	blood
36	chr11:9862400-9869200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr11:9862600-9873200	Strong transcription	Fetal Intestine Large	intestine
38	chr11:9862800-9868400	Weak transcription	HSMM	muscle
39	chr11:9863000-9869000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr11:9863000-9871200	Strong transcription	Primary monocytes fromperipheralblood	blood
41	chr11:9863000-9879800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr11:9863200-9868200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr11:9863200-9869000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr11:9863200-9869000	Strong transcription	Fetal Muscle Trunk	muscle
45	chr11:9863200-9876800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
46	chr11:9863400-9876000	Weak transcription	Primary T cells fromperipheralblood	blood
47	chr11:9863400-9877600	Weak transcription	HMEC	breast
48	chr11:9863400-9880000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
49	chr11:9863600-9879800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
50	chr11:9863800-9883800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood

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