Variant report

Variant	rs3915868
Chromosome Location	chr11:8833800-8833801
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	RCOR1	chr11:8833756-8833815	K562	blood:	n/a	n/a
2	TCF7L2	chr11:8833673-8834340	PANC-1	pancreas:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:8830703..8833043-chr11:8833134..8835525,2	MCF-7	breast:
2	chr11:8702847..8705692-chr11:8833365..8835740,2	MCF-7	breast:
3	chr11:8707539..8711325-chr11:8831652..8835543,5	MCF-7	breast:
4	chr11:8717868..8722426-chr11:8832973..8835335,4	K562	blood:

Variant related genes	Relation type
ST5	TF binding region
ENSG00000166441	Chromatin interaction
ENSG00000166444	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10522860	0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs10734638	0.89[CEU][hapmap]
rs10840127	0.95[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10840129	0.95[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11042070	0.90[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs11042072	0.90[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs11042099	0.89[CEU][hapmap];0.81[AMR][1000 genomes]
rs1133833	0.89[CEU][hapmap]
rs16906056	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17337866	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2568029	0.89[CEU][hapmap];0.90[MEX][hapmap]
rs2568035	0.84[CEU][hapmap]
rs2568056	0.89[CEU][hapmap]
rs2653558	0.89[CEU][hapmap]
rs2653591	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2742502	0.89[CEU][hapmap];0.80[MEX][hapmap]
rs34023999	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34033747	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34275210	0.83[AMR][1000 genomes]
rs34417491	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34418236	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs35503692	0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs35563381	0.82[AMR][1000 genomes]
rs35909878	0.83[AMR][1000 genomes]
rs36094920	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs36180552	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs3850934	0.92[CEU][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4390341	0.82[ASN][1000 genomes]
rs4910068	0.89[CEU][hapmap];0.90[MEX][hapmap]
rs4929915	1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7117900	0.89[CEU][hapmap]
rs7127197	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7936201	0.85[MEX][hapmap]
rs7950491	0.85[CEU][hapmap];0.82[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758256	chr11:8784813-9009573	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	esv2759803	chr11:8784813-9009573	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv527920	chr11:8816695-8856822	Weak transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv527073	chr11:8829168-8848463	Flanking Active TSS Active TSS Genic enhancers Enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs3915868	PRKCDBP	cis	parietal	SCAN
rs3915868	AMPD3	cis	parietal	SCAN
rs3915868	RPL27A	cis	parietal	SCAN
rs3915868	OR52A1	cis	parietal	SCAN
rs3915868	TMEM9B	cis	parietal	SCAN
rs3915868	C11orf17	cis	cerebellum	SCAN
rs3915868	RPL27A	cis	cerebellum	SCAN

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:8832200-8835000	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr11:8832400-8834600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr11:8832400-8835000	Weak transcription	HUVEC	blood vessel
4	chr11:8832400-8836800	Enhancers	Placenta Amnion	Placenta Amnion
5	chr11:8832600-8833800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr11:8832600-8834200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr11:8832600-8834600	Enhancers	Primary neutrophils fromperipheralblood	blood
8	chr11:8832600-8835000	Weak transcription	Primary hematopoietic stem cells	blood
9	chr11:8832600-8835200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr11:8832600-8840800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr11:8832800-8834400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr11:8832800-8835000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
13	chr11:8832800-8835400	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr11:8832800-8837400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
15	chr11:8833000-8833800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr11:8833000-8834200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr11:8833000-8834200	Weak transcription	Fetal Intestine Large	intestine
18	chr11:8833000-8834400	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr11:8833000-8834800	Enhancers	Adipose Nuclei	Adipose
20	chr11:8833000-8834800	Enhancers	Hela-S3	cervix
21	chr11:8833000-8835000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr11:8833000-8835000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr11:8833000-8835000	Weak transcription	HUES64 Cell Line	embryonic stem cell
24	chr11:8833000-8835400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr11:8833000-8835400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
26	chr11:8833000-8835400	Weak transcription	Duodenum Mucosa	Duodenum
27	chr11:8833000-8835400	Weak transcription	Left Ventricle	heart
28	chr11:8833000-8835400	Weak transcription	Psoas Muscle	Psoas
29	chr11:8833000-8835400	Weak transcription	Right Atrium	heart
30	chr11:8833000-8835400	Weak transcription	Right Ventricle	heart
31	chr11:8833000-8835400	Weak transcription	Small Intestine	intestine
32	chr11:8833000-8835400	Weak transcription	Spleen	Spleen
33	chr11:8833000-8836200	Enhancers	Stomach Mucosa	stomach
34	chr11:8833000-8836400	Enhancers	Colon Smooth Muscle	Colon
35	chr11:8833000-8837200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr11:8833000-8837200	Enhancers	NHDF-Ad	bronchial
37	chr11:8833000-8837400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr11:8833000-8837600	Enhancers	NHLF	lung
39	chr11:8833000-8839200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr11:8833200-8833800	Enhancers	HSMM	muscle
41	chr11:8833200-8834000	Enhancers	Brain Anterior Caudate	brain
42	chr11:8833200-8834000	Enhancers	Duodenum Smooth Muscle	Duodenum
43	chr11:8833200-8834200	Weak transcription	Placenta	Placenta
44	chr11:8833200-8834400	Weak transcription	Fetal Intestine Small	intestine
45	chr11:8833200-8834400	Weak transcription	Pancreatic Islets	Pancreatic Islet
46	chr11:8833200-8834400	Enhancers	HepG2	liver
47	chr11:8833200-8834800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr11:8833200-8834800	Weak transcription	HUES48 Cell Line	embryonic stem cell
49	chr11:8833200-8834800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
50	chr11:8833200-8834800	Weak transcription	Fetal Muscle Leg	muscle

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