Variant report

Variant	rs2187041
Chromosome Location	chr11:66534516-66534517
allele	A/G
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	STAT3	chr11:66534262-66534590	MCF10A-Er-Src	breast:	n/a	chr11:66534361-66534369

No.	Distal block	Cell Line	Cell type
1	chr11:66508922..66512626-chr11:66532752..66535976,6	MCF-7	breast:
2	chr11:66531934..66534799-chr11:66536564..66539469,2	MCF-7	breast:
3	chr11:66534456..66536238-chr11:66540459..66542378,3	K562	blood:
4	chr11:66495562..66497940-chr11:66534176..66536723,2	K562	blood:
5	chr11:66531006..66534192-chr11:66534200..66538203,4	K562	blood:
6	chr11:66531067..66535329-chr11:66536471..66539126,4	K562	blood:

Variant related genes	Relation type
ENSG00000213409	TF binding region
ENSG00000173898	Chromatin interaction
ENSG00000254984	Chromatin interaction
ENSG00000173715	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10160758	0.85[ASW][hapmap];0.81[CEU][hapmap];0.83[GIH][hapmap];0.84[MEX][hapmap];0.85[TSI][hapmap]
rs10750790	1.00[ASW][hapmap];0.95[CEU][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10791889	1.00[ASW][hapmap];0.95[CEU][hapmap];0.86[CHB][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap]
rs10791890	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10791891	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10791892	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10896135	1.00[CEU][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10896139	0.90[CEU][hapmap];0.88[GIH][hapmap];0.86[MEX][hapmap];0.88[TSI][hapmap];0.83[EUR][1000 genomes]
rs11227610	0.81[CEU][hapmap];0.82[YRI][hapmap];0.87[EUR][1000 genomes]
rs11600959	0.93[ASW][hapmap];0.85[CEU][hapmap];0.83[GIH][hapmap];0.83[TSI][hapmap];0.86[EUR][1000 genomes]
rs2077432	0.95[CEU][hapmap];0.83[GIH][hapmap];0.86[MEX][hapmap];0.85[TSI][hapmap];0.86[EUR][1000 genomes]
rs2167457	0.86[ASW][hapmap];0.90[CEU][hapmap];0.83[GIH][hapmap];0.86[MEX][hapmap];0.85[TSI][hapmap];0.84[EUR][1000 genomes]
rs2242663	0.86[ASW][hapmap];0.80[MEX][hapmap]
rs3741194	0.90[CEU][hapmap];0.83[GIH][hapmap];0.83[EUR][1000 genomes]
rs3741364	1.00[ASW][hapmap];1.00[JPT][hapmap];0.80[MKK][hapmap];0.86[YRI][hapmap];0.80[ASN][1000 genomes]
rs4576826	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4930184	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4930390	1.00[ASW][hapmap];0.95[CEU][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.95[TSI][hapmap];0.86[YRI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6591222	0.90[CEU][hapmap];0.89[GIH][hapmap];0.80[MEX][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7103627	0.81[CEU][hapmap];0.83[GIH][hapmap];0.81[TSI][hapmap];0.81[EUR][1000 genomes]
rs7119426	0.90[CEU][hapmap];0.83[GIH][hapmap];0.86[MEX][hapmap];0.88[TSI][hapmap];0.85[EUR][1000 genomes]
rs7120256	0.90[CEU][hapmap];0.83[GIH][hapmap];0.85[TSI][hapmap];0.85[EUR][1000 genomes]
rs7122539	0.83[TSI][hapmap]
rs714766	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7570	0.95[CEU][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7930203	1.00[ASW][hapmap];0.95[CEU][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.95[TSI][hapmap];0.86[YRI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7948839	0.85[CEU][hapmap];0.80[TSI][hapmap];0.81[EUR][1000 genomes]
rs9971487	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv897789	chr11:66372390-66634397	Weak transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
2	nsv897790	chr11:66414915-66626234	Transcr. at gene 5' and 3' Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
3	nsv427891	chr11:66456140-66606701	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
4	nsv468602	chr11:66468469-66634397	Enhancers Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Weak 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	70 gene(s)	inside rSNPs	diseases
5	nsv555225	chr11:66468469-66634397	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
6	esv1798614	chr11:66514847-66535177	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	nsv516087	chr11:66516049-66579572	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2187041	CTSF	cis	Whole Blood	GTEx
rs2187041	LRFN4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:66513200-66541200	Weak transcription	Aorta	Aorta
2	chr11:66513200-66555000	Weak transcription	Pancreas	Pancrea
3	chr11:66513400-66540800	Weak transcription	Spleen	Spleen
4	chr11:66513400-66547800	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr11:66513400-66606800	Weak transcription	Brain Angular Gyrus	brain
6	chr11:66513600-66538800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
7	chr11:66513800-66539800	Weak transcription	GM12878-XiMat	blood
8	chr11:66515400-66535800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr11:66516600-66542200	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr11:66516800-66535000	Weak transcription	HMEC	breast
11	chr11:66516800-66535200	Weak transcription	Fetal Brain Male	brain
12	chr11:66517400-66535200	Weak transcription	Osteobl	bone
13	chr11:66524000-66540600	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr11:66524000-66542200	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr11:66525400-66535000	Weak transcription	A549	lung
16	chr11:66525600-66538400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr11:66526400-66541400	Weak transcription	Small Intestine	intestine
18	chr11:66526600-66549800	Weak transcription	Lung	lung
19	chr11:66527000-66540200	Weak transcription	Primary T cells fromperipheralblood	blood
20	chr11:66527000-66574200	Weak transcription	Primary T helper cells fromperipheralblood	blood
21	chr11:66527000-66595600	Weak transcription	HSMM	muscle
22	chr11:66527200-66539600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr11:66527400-66571600	Weak transcription	Primary T cells from cord blood	blood
24	chr11:66527800-66539600	Weak transcription	Adipose Nuclei	Adipose
25	chr11:66529400-66540400	Weak transcription	Duodenum Mucosa	Duodenum
26	chr11:66529400-66541000	Weak transcription	Dnd41	blood
27	chr11:66529800-66542000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr11:66530000-66559000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr11:66530000-66571400	Weak transcription	Fetal Muscle Trunk	muscle
30	chr11:66530000-66605400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr11:66530200-66535000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr11:66530200-66540800	Weak transcription	Rectal Mucosa Donor 31	rectum
33	chr11:66530200-66549800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr11:66530200-66556000	Weak transcription	Gastric	stomach
35	chr11:66530200-66582400	Weak transcription	HUVEC	blood vessel
36	chr11:66530400-66536200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr11:66530600-66551200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr11:66530600-66555800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr11:66530600-66575200	Weak transcription	Esophagus	oesophagus
40	chr11:66530600-66600000	Weak transcription	Fetal Muscle Leg	muscle
41	chr11:66530800-66581800	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr11:66531000-66534800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr11:66531000-66535200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
44	chr11:66531000-66572800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
45	chr11:66531200-66577800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr11:66531400-66537400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr11:66531400-66555200	Weak transcription	Stomach Smooth Muscle	stomach
48	chr11:66531400-66555800	Weak transcription	Fetal Intestine Small	intestine
49	chr11:66531400-66557000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr11:66531400-66578000	Weak transcription	Cortex derived primary cultured neurospheres	brain

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