Variant report

Variant	rs677298
Chromosome Location	chr11:64564208-64564209
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:64544185..64546327-chr11:64562528..64564348,2	K562	blood:
2	chr11:64561801..64564643-chr11:64576528..64579219,3	MCF-7	breast:
3	chr11:64562357..64564495-chr11:64608221..64612051,3	MCF-7	breast:
4	chr11:64562935..64566050-chr11:64567967..64570422,3	K562	blood:

Variant related genes	Relation type
ENSG00000168067	Chromatin interaction
ENSG00000133895	Chromatin interaction
ENSG00000171219	Chromatin interaction
ENSG00000168066	Chromatin interaction

Extended variants
information (count: 68 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10897524	0.84[GIH][hapmap]
rs10897525	0.84[JPT][hapmap];0.83[MEX][hapmap]
rs11231853	0.86[CEU][hapmap]
rs11231859	1.00[CEU][hapmap]
rs11231869	0.83[MEX][hapmap]
rs1143937	1.00[CEU][hapmap];0.85[CHB][hapmap];0.85[GIH][hapmap];0.89[JPT][hapmap];0.94[MEX][hapmap];0.92[TSI][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12223914	0.80[AMR][1000 genomes]
rs1633462	1.00[CEU][hapmap];0.85[AMR][1000 genomes]
rs17146121	1.00[ASW][hapmap];0.89[CEU][hapmap];0.85[GIH][hapmap];0.83[MEX][hapmap]
rs2073798	0.92[GIH][hapmap]
rs2267918	1.00[CEU][hapmap]
rs2284301	1.00[CEU][hapmap]
rs2959652	1.00[CEU][hapmap];0.92[GIH][hapmap]
rs3741398	1.00[CEU][hapmap];0.80[CHB][hapmap];0.88[MEX][hapmap]
rs3809076	0.89[CEU][hapmap];0.83[MEX][hapmap]
rs474707	0.81[CEU][hapmap];0.83[MEX][hapmap];0.81[AMR][1000 genomes]
rs476037	1.00[ASW][hapmap];0.89[CEU][hapmap];0.85[GIH][hapmap];0.83[MEX][hapmap]
rs477549	1.00[CEU][hapmap];0.83[MEX][hapmap];0.81[AMR][1000 genomes]
rs483962	1.00[CEU][hapmap];0.83[MEX][hapmap]
rs487105	1.00[CEU][hapmap];0.88[MEX][hapmap];0.85[AMR][1000 genomes]
rs489192	1.00[CEU][hapmap]
rs490980	0.89[CEU][hapmap]
rs496914	1.00[CEU][hapmap]
rs509606	0.88[AMR][1000 genomes]
rs523200	1.00[CEU][hapmap]
rs532747	0.83[MEX][hapmap];0.83[AMR][1000 genomes]
rs547066	0.92[GIH][hapmap];0.87[MEX][hapmap];0.83[AMR][1000 genomes]
rs569602	0.83[MEX][hapmap];0.80[AMR][1000 genomes]
rs582980	0.87[EUR][1000 genomes]
rs589691	1.00[CEU][hapmap];0.92[GIH][hapmap]
rs593394	0.85[AMR][1000 genomes]
rs606458	1.00[CEU][hapmap]
rs607389	1.00[CEU][hapmap];0.84[CHB][hapmap];0.84[JPT][hapmap];0.81[EUR][1000 genomes]
rs624975	0.90[CEU][hapmap];0.89[GIH][hapmap];0.89[JPT][hapmap];0.94[MEX][hapmap];0.92[TSI][hapmap];0.89[AMR][1000 genomes]
rs625172	0.92[GIH][hapmap]
rs637332	1.00[CEU][hapmap];0.83[MEX][hapmap];0.81[AMR][1000 genomes]
rs669976	0.90[CEU][hapmap];0.85[CHB][hapmap];0.85[GIH][hapmap];0.84[JPT][hapmap];0.94[MEX][hapmap];0.92[TSI][hapmap];0.91[AMR][1000 genomes]
rs674297	0.87[AMR][1000 genomes]
rs67808744	0.94[AMR][1000 genomes]
rs680273	1.00[CEU][hapmap]
rs683841	0.85[AMR][1000 genomes]
rs684720	0.87[AMR][1000 genomes]
rs686171	0.83[AMR][1000 genomes]
rs693235	0.90[CEU][hapmap]
rs72643568	0.81[AMR][1000 genomes]
rs7939965	0.89[CEU][hapmap];0.85[GIH][hapmap];0.83[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:22 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv897694	chr11:64334114-64584959	Weak transcription Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
2	nsv528506	chr11:64345448-64701030	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1075 gene(s)	inside rSNPs	diseases
3	nsv897695	chr11:64357072-64701030	Weak transcription Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1075 gene(s)	inside rSNPs	diseases
4	nsv555198	chr11:64373899-64573589	Weak transcription Transcr. at gene 5' and 3' Genic enhancers Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
5	nsv897697	chr11:64447420-64584959	Flanking Bivalent TSS/Enh Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
6	nsv897698	chr11:64447420-64621573	Active TSS Bivalent Enhancer Genic enhancers Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
7	nsv897699	chr11:64447420-64638041	Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
8	nsv897700	chr11:64447420-64701030	Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1071 gene(s)	inside rSNPs	diseases
9	nsv555202	chr11:64477050-64573589	Strong transcription Bivalent/Poised TSS Enhancers Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
10	nsv468597	chr11:64477050-64584959	Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
11	nsv468598	chr11:64477050-64584959	Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Active TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
12	nsv555203	chr11:64477050-64584959	Strong transcription Genic enhancers Bivalent Enhancer Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
13	nsv1049744	chr11:64486615-64630149	Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Weak transcription Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
14	nsv832189	chr11:64487183-64620199	Weak transcription Transcr. at gene 5' and 3' Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
15	nsv469962	chr11:64527080-64621573	Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
16	nsv897702	chr11:64532579-64584231	Transcr. at gene 5' and 3' Strong transcription Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
17	nsv897703	chr11:64538346-64574200	Strong transcription Transcr. at gene 5' and 3' Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
18	nsv519117	chr11:64546391-64573589	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
19	nsv519478	chr11:64546391-64584987	Flanking Active TSS Enhancers Weak transcription Strong transcription 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	49 gene(s)	inside rSNPs	diseases
20	nsv555204	chr11:64561200-64574200	Strong transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
21	nsv555205	chr11:64561200-64575505	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
22	nsv555206	chr11:64563757-64574200	Strong transcription Flanking Active TSS Weak transcription Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs677298	SF1	Cis_1M	lymphoblastoid	RTeQTL
rs677298	SF1	cis	multi-tissue	Pritchard
rs677298	SF1	cis	lymphoblastoid	seeQTL

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:64547200-64569600	Weak transcription	Small Intestine	intestine
2	chr11:64547200-64569600	Weak transcription	NH-A	brain
3	chr11:64547200-64569800	Weak transcription	Osteobl	bone
4	chr11:64547200-64570000	Weak transcription	Fetal Kidney	kidney
5	chr11:64547400-64569600	Weak transcription	HUES64 Cell Line	embryonic stem cell
6	chr11:64547400-64569800	Weak transcription	NHEK	skin
7	chr11:64547600-64567000	Weak transcription	HUVEC	blood vessel
8	chr11:64547600-64569800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr11:64547800-64568800	Weak transcription	Dnd41	blood
10	chr11:64548800-64568800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr11:64550200-64569400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr11:64550400-64570000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr11:64553800-64568800	Strong transcription	Fetal Stomach	stomach
14	chr11:64555400-64568600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr11:64555400-64568800	Strong transcription	Thymus	Thymus
16	chr11:64555400-64569400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr11:64555400-64570000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr11:64555600-64567600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr11:64555600-64568600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
20	chr11:64555600-64569000	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr11:64555600-64569800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr11:64555800-64565400	Strong transcription	Monocytes-CD14+_RO01746	blood
23	chr11:64555800-64567600	Strong transcription	Primary monocytes fromperipheralblood	blood
24	chr11:64555800-64569000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
25	chr11:64556000-64565200	Strong transcription	Gastric	stomach
26	chr11:64556000-64569000	Strong transcription	Cortex derived primary cultured neurospheres	brain
27	chr11:64557200-64565400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr11:64557800-64569600	Weak transcription	Rectal Mucosa Donor 29	rectum
29	chr11:64558000-64569000	Strong transcription	Fetal Intestine Small	intestine
30	chr11:64558200-64570000	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr11:64560200-64565200	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
32	chr11:64560600-64564600	Genic enhancers	Primary T cells fromperipheralblood	blood
33	chr11:64560600-64565200	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr11:64560800-64567800	Strong transcription	Stomach Smooth Muscle	stomach
35	chr11:64561400-64569400	Weak transcription	Stomach Mucosa	stomach
36	chr11:64561600-64570000	Weak transcription	Fetal Heart	heart
37	chr11:64562000-64570000	Weak transcription	H1 Cell Line	embryonic stem cell
38	chr11:64562000-64570000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr11:64562200-64564400	Genic enhancers	Fetal Muscle Leg	muscle
40	chr11:64562200-64566800	Strong transcription	Brain Substantia Nigra	brain
41	chr11:64562600-64566400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
42	chr11:64562800-64568600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr11:64563000-64569600	Weak transcription	NHDF-Ad	bronchial
44	chr11:64563200-64564400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
45	chr11:64563200-64564400	Strong transcription	Liver	Liver
46	chr11:64563200-64564400	Genic enhancers	Fetal Muscle Trunk	muscle
47	chr11:64563200-64564600	Genic enhancers	Primary T cells from cord blood	blood
48	chr11:64563200-64564600	Strong transcription	Pancreas	Pancrea
49	chr11:64563200-64564800	Strong transcription	HUES6 Cell Line	embryonic stem cell
50	chr11:64563200-64565000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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