Variant report

Variant	rs10899079
Chromosome Location	chr11:74874433-74874434
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	ELF1	chr11:74874384-74874711	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:74856790..74858510-chr11:74872953..74874736,2	K562	blood:
2	chr11:74868174..74871042-chr11:74871954..74874502,2	K562	blood:

Variant related genes	Relation type
SLCO2B1	TF binding region
ENSG00000137491	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10793114	0.82[AMR][1000 genomes]
rs10899076	0.83[MEX][hapmap];0.82[AMR][1000 genomes]
rs10899078	0.86[CHB][hapmap];0.82[CHD][hapmap];0.85[JPT][hapmap]
rs11236348	0.81[AMR][1000 genomes]
rs11236349	0.81[AMR][1000 genomes]
rs11236350	0.83[MEX][hapmap];0.85[AMR][1000 genomes]
rs11236351	0.81[AMR][1000 genomes]
rs11236352	0.81[AMR][1000 genomes]
rs11236353	0.81[AMR][1000 genomes]
rs11236354	0.82[AMR][1000 genomes]
rs11236356	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11236357	0.86[CHB][hapmap];0.88[CHD][hapmap];0.90[JPT][hapmap];0.87[MEX][hapmap];0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs11236358	0.93[ASN][1000 genomes]
rs11236361	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11236365	0.80[JPT][hapmap]
rs11822379	0.82[AMR][1000 genomes]
rs11827488	0.92[CEU][hapmap]
rs12361277	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12422149	0.80[JPT][hapmap]
rs17133732	0.88[CEU][hapmap]
rs3740839	0.89[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.92[TSI][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4100076	1.00[CEU][hapmap];0.86[CHB][hapmap];0.92[CHD][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4397881	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4944073	1.00[CEU][hapmap];0.90[CHB][hapmap];0.94[CHD][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4944074	0.80[JPT][hapmap]
rs4944974	0.89[CEU][hapmap];0.84[TSI][hapmap]
rs4944990	0.82[AMR][1000 genomes]
rs4944992	0.86[CHB][hapmap];0.81[CHD][hapmap];0.85[JPT][hapmap]
rs4944993	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4944994	0.86[CHB][hapmap];0.85[CHD][hapmap];0.90[JPT][hapmap];0.92[MEX][hapmap];0.90[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs57073688	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6592602	0.89[CEU][hapmap];0.92[TSI][hapmap]
rs67904312	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs67947132	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7125268	0.80[JPT][hapmap]
rs72996586	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs72998525	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs881217	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs949069	0.91[CHB][hapmap];0.90[CHD][hapmap];0.82[GIH][hapmap];0.90[JPT][hapmap];0.87[MEX][hapmap];0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv897919	chr11:74862391-74875501	Flanking Active TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
2	nsv1054122	chr11:74872792-74895241	Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs10899079	FCHSD2	cis	cerebellum	SCAN
rs10899079	PGM2L1	cis	cerebellum	SCAN
rs10899079	KCTD21	cis	cerebellum	SCAN
rs10899079	BTAF1	trans	cerebellum	SCAN
rs10899079	USP35	cis	cerebellum	SCAN
rs10899079	GDPD4	cis	cerebellum	SCAN

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:74863600-74885600	Weak transcription	Colon Smooth Muscle	Colon
2	chr11:74864200-74898400	Weak transcription	Esophagus	oesophagus
3	chr11:74867600-74875000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr11:74868600-74875200	Weak transcription	Ovary	ovary
5	chr11:74870000-74881000	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr11:74870400-74875000	Weak transcription	Small Intestine	intestine
7	chr11:74870800-74901600	Weak transcription	Rectal Smooth Muscle	rectum
8	chr11:74871400-74875200	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr11:74871400-74886800	Weak transcription	Brain Substantia Nigra	brain
10	chr11:74871600-74875000	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr11:74871600-74875600	Enhancers	HepG2	liver
12	chr11:74872200-74885400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr11:74872400-74875400	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr11:74872400-74876400	Enhancers	Placenta	Placenta
15	chr11:74872400-74883600	Genic enhancers	Fetal Intestine Small	intestine
16	chr11:74872600-74874800	Enhancers	Stomach Mucosa	stomach
17	chr11:74872600-74877200	Enhancers	Fetal Muscle Leg	muscle
18	chr11:74872800-74878200	Enhancers	Fetal Muscle Trunk	muscle
19	chr11:74872800-74878800	Genic enhancers	Fetal Intestine Large	intestine
20	chr11:74873000-74876200	Enhancers	Right Ventricle	heart
21	chr11:74873200-74874600	Weak transcription	Fetal Stomach	stomach
22	chr11:74873200-74875200	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr11:74873200-74875400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr11:74873200-74877800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr11:74873400-74874600	Weak transcription	Left Ventricle	heart
26	chr11:74873400-74875000	Strong transcription	Sigmoid Colon	Sigmoid Colon
27	chr11:74873400-74875400	Enhancers	Skeletal Muscle Male	skeletal muscle
28	chr11:74873400-74879400	Weak transcription	Adipose Nuclei	Adipose
29	chr11:74873600-74874600	Weak transcription	Brain Hippocampus Middle	brain
30	chr11:74873800-74875000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr11:74873800-74875400	Weak transcription	Colonic Mucosa	Colon
32	chr11:74873800-74875600	Weak transcription	Fetal Thymus	thymus
33	chr11:74874000-74874600	Weak transcription	Pancreas	Pancrea
34	chr11:74874000-74874600	Weak transcription	Rectal Mucosa Donor 31	rectum
35	chr11:74874000-74874800	Weak transcription	Lung	lung
36	chr11:74874000-74875000	Weak transcription	Spleen	Spleen
37	chr11:74874000-74875600	Flanking Active TSS	Liver	Liver
38	chr11:74874000-74878000	Weak transcription	Gastric	stomach
39	chr11:74874000-74885800	Weak transcription	Brain Cingulate Gyrus	brain
40	chr11:74874200-74875600	Enhancers	Duodenum Mucosa	Duodenum

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