Variant report

Variant	rs615536
Chromosome Location	chr11:66481264-66481265
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	POLR2A	chr11:66481165-66481400	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:66480301..66482694-chr11:66511390..66512916,2	MCF-7	breast:
2	chr11:66480809..66482558-chr11:66795505..66798066,2	MCF-7	breast:
3	chr11:66464609..66468025-chr11:66478918..66483442,5	MCF-7	breast:

Variant related genes	Relation type
RN7SL12P	TF binding region
ENSG00000173227	Chromatin interaction
ENSG00000173898	Chromatin interaction
ENSG00000173715	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs1110708	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs17582367	1.00[GIH][hapmap]
rs470300	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.80[MKK][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs664297	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][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	nsv522277	chr11:66234023-66493825	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
2	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
3	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
4	nsv897791	chr11:66442855-66533469	Weak transcription Strong transcription Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
5	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
6	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
7	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs615536	RIN1	cis	multi-tissue	Pritchard

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:66446200-66485800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr11:66452200-66485600	Strong transcription	HUES48 Cell Line	embryonic stem cell
3	chr11:66453000-66483400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
4	chr11:66456400-66494600	Weak transcription	Right Atrium	heart
5	chr11:66462600-66484000	Weak transcription	Brain Substantia Nigra	brain
6	chr11:66462800-66484400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr11:66463000-66485000	Weak transcription	Fetal Muscle Trunk	muscle
8	chr11:66465600-66487000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr11:66467400-66485200	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr11:66468400-66484600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr11:66468800-66481400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr11:66468800-66481800	Weak transcription	Spleen	Spleen
13	chr11:66468800-66487800	Strong transcription	Fetal Brain Female	brain
14	chr11:66469600-66486800	Weak transcription	A549	lung
15	chr11:66469800-66484800	Weak transcription	HepG2	liver
16	chr11:66471600-66489200	Strong transcription	Brain Germinal Matrix	brain
17	chr11:66471800-66483200	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr11:66471800-66483400	Strong transcription	Cortex derived primary cultured neurospheres	brain
19	chr11:66471800-66483600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr11:66471800-66483600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
21	chr11:66471800-66485000	Strong transcription	H1 Cell Line	embryonic stem cell
22	chr11:66472000-66483400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr11:66472000-66483400	Strong transcription	Esophagus	oesophagus
24	chr11:66472000-66483600	Strong transcription	HUES6 Cell Line	embryonic stem cell
25	chr11:66472200-66483200	Strong transcription	Pancreas	Pancrea
26	chr11:66473000-66484200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr11:66473000-66485600	Weak transcription	Duodenum Mucosa	Duodenum
28	chr11:66473400-66484800	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr11:66473600-66481400	Weak transcription	Gastric	stomach
30	chr11:66473600-66484400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr11:66474600-66483600	Strong transcription	HUES64 Cell Line	embryonic stem cell
32	chr11:66476000-66485000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr11:66476400-66481400	Weak transcription	Brain Angular Gyrus	brain
34	chr11:66477200-66482800	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr11:66477600-66483600	Strong transcription	Liver	Liver
36	chr11:66477800-66483000	Strong transcription	Placenta Amnion	Placenta Amnion
37	chr11:66478000-66481400	Strong transcription	Fetal Stomach	stomach
38	chr11:66478000-66483200	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr11:66478400-66484200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr11:66478400-66486600	Weak transcription	Hela-S3	cervix
41	chr11:66478600-66484800	Weak transcription	Lung	lung
42	chr11:66479200-66483200	Strong transcription	K562	blood
43	chr11:66479200-66485000	Weak transcription	Fetal Intestine Large	intestine
44	chr11:66479400-66483600	Strong transcription	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr11:66480000-66483000	Strong transcription	NHEK	skin
46	chr11:66480200-66481800	Strong transcription	Fetal Brain Male	brain
47	chr11:66480200-66482600	Strong transcription	Brain Cingulate Gyrus	brain
48	chr11:66480200-66482800	Strong transcription	Fetal Kidney	kidney
49	chr11:66480200-66483200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr11:66480400-66482200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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