Variant report

Variant	rs10899379
Chromosome Location	chr11:77169671-77169672
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:77168519..77171597-chr11:77180665..77182753,3	MCF-7	breast:
2	chr11:77168629..77170251-chr11:77183087..77185478,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000149269	Chromatin interaction
ENSG00000268635	Chromatin interaction

Extended variants
information (count: 99 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:91)

rs_ID	r²[population]
rs10793248	0.84[ASN][1000 genomes]
rs10899376	0.95[CEU][hapmap];0.93[EUR][1000 genomes]
rs10899378	0.97[EUR][1000 genomes]
rs11237173	0.93[EUR][1000 genomes]
rs11237189	0.97[EUR][1000 genomes]
rs11237193	0.97[EUR][1000 genomes]
rs11237195	0.90[CEU][hapmap];0.96[EUR][1000 genomes]
rs11237196	0.96[EUR][1000 genomes]
rs11237199	0.84[CEU][hapmap];0.88[EUR][1000 genomes]
rs12271542	0.96[EUR][1000 genomes]
rs12420360	0.90[YRI][hapmap]
rs1377470	0.95[CEU][hapmap];0.92[EUR][1000 genomes]
rs1377471	0.92[EUR][1000 genomes]
rs1453343	0.86[EUR][1000 genomes]
rs1670459	0.86[CHB][hapmap];0.87[JPT][hapmap]
rs1793476	0.86[CHB][hapmap];0.87[JPT][hapmap]
rs1793483	0.86[CHB][hapmap];0.87[JPT][hapmap]
rs1840151	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2250639	0.96[CEU][hapmap];0.92[EUR][1000 genomes]
rs2250647	0.95[CEU][hapmap];0.92[EUR][1000 genomes]
rs2298793	0.95[CEU][hapmap];0.92[EUR][1000 genomes]
rs2602458	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2602459	0.91[EUR][1000 genomes]
rs2602462	0.81[AFR][1000 genomes]
rs2602463	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2602464	0.96[CEU][hapmap];0.92[EUR][1000 genomes]
rs2602465	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2602468	0.92[EUR][1000 genomes]
rs2602469	0.92[EUR][1000 genomes]
rs2602470	0.92[EUR][1000 genomes]
rs2602472	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2602473	0.87[YRI][hapmap]
rs2602477	0.96[EUR][1000 genomes]
rs2602479	0.96[EUR][1000 genomes]
rs2602488	0.91[CEU][hapmap];0.85[EUR][1000 genomes]
rs2602489	0.86[EUR][1000 genomes]
rs2725810	0.95[CEU][hapmap];0.95[EUR][1000 genomes]
rs2725812	0.82[JPT][hapmap]
rs2725815	0.86[EUR][1000 genomes]
rs2725816	0.93[EUR][1000 genomes]
rs2725826	0.86[EUR][1000 genomes]
rs2725827	0.96[CEU][hapmap];0.93[EUR][1000 genomes]
rs2725830	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2725831	0.93[EUR][1000 genomes]
rs2725832	0.91[EUR][1000 genomes]
rs2729747	0.83[AFR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2729753	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2729762	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.96[YRI][hapmap];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2729769	0.86[EUR][1000 genomes]
rs2729771	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2844328	0.96[EUR][1000 genomes]
rs2844332	0.96[EUR][1000 genomes]
rs2844333	1.00[CEU][hapmap];0.95[CHB][hapmap];0.92[JPT][hapmap];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2844334	0.95[CEU][hapmap];0.95[EUR][1000 genomes]
rs2844336	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2844337	0.95[CEU][hapmap];0.86[EUR][1000 genomes]
rs2852384	0.96[EUR][1000 genomes]
rs2852385	0.91[EUR][1000 genomes]
rs2852388	0.84[YRI][hapmap]
rs2852389	0.85[AFR][1000 genomes]
rs2852390	0.89[YRI][hapmap];0.84[AFR][1000 genomes]
rs2852392	0.95[CEU][hapmap];0.88[EUR][1000 genomes]
rs2852394	0.96[EUR][1000 genomes]
rs2853086	0.95[EUR][1000 genomes]
rs2853087	0.96[EUR][1000 genomes]
rs2853088	0.94[EUR][1000 genomes]
rs2853090	0.93[EUR][1000 genomes]
rs2853103	0.90[CEU][hapmap];0.91[EUR][1000 genomes]
rs3015984	0.83[ASN][1000 genomes]
rs3015989	0.95[JPT][hapmap]
rs3015993	0.95[JPT][hapmap]
rs3019240	0.83[ASN][1000 genomes]
rs3019258	0.84[ASN][1000 genomes]
rs4590893	0.94[EUR][1000 genomes]
rs476925	0.87[JPT][hapmap]
rs4945166	0.83[JPT][hapmap]
rs495889	0.95[JPT][hapmap]
rs514191	0.83[CHB][hapmap];0.88[JPT][hapmap]
rs575662	0.82[CHB][hapmap];0.87[JPT][hapmap]
rs599437	0.87[JPT][hapmap]
rs628325	0.84[ASN][1000 genomes]
rs6592721	0.83[AFR][1000 genomes]
rs674652	0.96[JPT][hapmap]
rs683497	0.84[ASN][1000 genomes]
rs688212	0.88[JPT][hapmap]
rs7109645	0.87[EUR][1000 genomes]
rs7112264	0.87[AFR][1000 genomes]
rs7118869	0.88[JPT][hapmap]
rs7119033	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7943778	0.85[EUR][1000 genomes]
rs947809	0.87[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1048360	chr11:76900813-77387933	Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv541089	chr11:76900813-77387933	Active TSS Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv1049603	chr11:76900813-77520411	Strong transcription Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	nsv541090	chr11:76900813-77520411	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
5	esv3424135	chr11:76961603-77277087	Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	nsv1037724	chr11:77061945-77250391	Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv541091	chr11:77061945-77250391	Weak transcription Active TSS Enhancers Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	esv3437433	chr11:77101280-77291686	Flanking Bivalent TSS/Enh Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:77155400-77181400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr11:77158400-77169800	Weak transcription	Fetal Intestine Large	intestine
3	chr11:77160600-77178000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr11:77161000-77170200	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr11:77161200-77179200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr11:77163000-77173400	Weak transcription	Placenta	Placenta
7	chr11:77164000-77169800	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr11:77165000-77172200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr11:77165200-77170800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr11:77165800-77171200	Enhancers	H1 Cell Line	embryonic stem cell
11	chr11:77166200-77172800	Enhancers	iPS-15b Cell Line	embryonic stem cell
12	chr11:77167800-77182000	Weak transcription	Fetal Kidney	kidney
13	chr11:77168000-77170400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
14	chr11:77168200-77170200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr11:77168400-77170600	Enhancers	Brain Hippocampus Middle	brain
16	chr11:77168400-77172200	Enhancers	Fetal Intestine Small	intestine
17	chr11:77168600-77170000	Weak transcription	Primary B cells from cord blood	blood
18	chr11:77168600-77170400	Enhancers	Stomach Mucosa	stomach
19	chr11:77168600-77173000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr11:77168600-77173600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr11:77168600-77178800	Weak transcription	Monocytes-CD14+_RO01746	blood
22	chr11:77168800-77170000	Weak transcription	Small Intestine	intestine
23	chr11:77168800-77170000	Weak transcription	NH-A	brain
24	chr11:77168800-77170400	Enhancers	ES-I3 Cell Line	embryonic stem cell
25	chr11:77168800-77170600	Weak transcription	Psoas Muscle	Psoas
26	chr11:77168800-77179600	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr11:77169000-77169800	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr11:77169000-77170000	Enhancers	iPS-18 Cell Line	embryonic stem cell
29	chr11:77169000-77170000	Weak transcription	Brain Germinal Matrix	brain
30	chr11:77169000-77170200	Weak transcription	Brain Anterior Caudate	brain
31	chr11:77169000-77171000	Enhancers	HUES6 Cell Line	embryonic stem cell
32	chr11:77169000-77173000	Enhancers	HUES64 Cell Line	embryonic stem cell
33	chr11:77169000-77174600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
34	chr11:77169000-77175200	Weak transcription	H9 Cell Line	embryonic stem cell
35	chr11:77169000-77181400	Weak transcription	Brain Angular Gyrus	brain
36	chr11:77169200-77169800	Weak transcription	Pancreatic Islets	Pancreatic Islet
37	chr11:77169200-77169800	Enhancers	GM12878-XiMat	blood
38	chr11:77169200-77173000	Enhancers	HUES48 Cell Line	embryonic stem cell
39	chr11:77169400-77170400	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
40	chr11:77169400-77170600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
41	chr11:77169600-77169800	Enhancers	Duodenum Mucosa	Duodenum
42	chr11:77169600-77170000	Enhancers	Brain Cingulate Gyrus	brain
43	chr11:77169600-77171000	Weak transcription	Brain Substantia Nigra	brain

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