Variant report

Variant	rs4944994
Chromosome Location	chr11:74869888-74869889
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:74868174..74870399-chr11:74871954..74873534,2	K562	blood:
2	chr11:74867339..74870278-chr11:74875624..74878251,3	K562	blood:
3	chr11:74869846..74870366-chr11:74959734..74960273,2	MCF-7	breast:
4	chr11:74869678..74870459-chr11:74915424..74916683,3	MCF-7	breast:
5	chr11:74866771..74870278-chr11:74874697..74878251,4	K562	blood:

Variant related genes	Relation type
ENSG00000137491	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10793114	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10899076	0.95[CEU][hapmap];0.87[CHB][hapmap];0.85[CHD][hapmap];0.93[GIH][hapmap];0.92[MEX][hapmap];0.94[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10899077	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10899078	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10899079	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]
rs11236348	0.93[CEU][hapmap];0.85[CHB][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11236349	1.00[CEU][hapmap];0.87[CHB][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11236350	0.95[CEU][hapmap];0.87[CHB][hapmap];0.85[CHD][hapmap];0.91[GIH][hapmap];0.92[MEX][hapmap];0.94[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11236351	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11236352	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11236353	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11236354	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11236356	0.91[CHB][hapmap];0.81[CHD][hapmap];0.80[GIH][hapmap];0.86[JPT][hapmap];0.80[MEX][hapmap]
rs11236357	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11236358	0.82[ASN][1000 genomes]
rs11236361	0.86[CHB][hapmap];0.87[CHD][hapmap];0.82[GIH][hapmap];0.91[JPT][hapmap];0.92[MEX][hapmap];0.90[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs11236365	0.86[CEU][hapmap];0.85[CHD][hapmap];0.91[JPT][hapmap];0.88[EUR][1000 genomes]
rs11822379	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12422149	0.91[JPT][hapmap]
rs3740839	0.86[CHB][hapmap];0.83[CHD][hapmap];0.91[JPT][hapmap];0.84[MEX][hapmap];0.81[ASN][1000 genomes]
rs4100076	0.82[CHB][hapmap];0.80[MEX][hapmap];0.81[AMR][1000 genomes]
rs4397881	0.91[CHB][hapmap];0.81[GIH][hapmap];0.91[JPT][hapmap];0.87[MEX][hapmap];0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4944073	0.85[CHB][hapmap];0.80[CHD][hapmap];0.86[JPT][hapmap];0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs4944074	0.95[CEU][hapmap];0.91[JPT][hapmap];0.84[TSI][hapmap];0.90[EUR][1000 genomes]
rs4944975	0.90[CEU][hapmap];0.90[TSI][hapmap]
rs4944990	0.95[CEU][hapmap];0.91[CHB][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4944991	1.00[CEU][hapmap];0.91[CHB][hapmap];0.90[CHD][hapmap];0.93[GIH][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4944992	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4944993	0.91[CHB][hapmap];0.81[CHD][hapmap];0.80[GIH][hapmap];0.86[JPT][hapmap];0.80[MEX][hapmap];0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs57073688	0.90[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs59633704	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs67904312	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs7125268	0.86[CEU][hapmap];0.85[CHD][hapmap];0.91[JPT][hapmap];0.81[TSI][hapmap];0.89[EUR][1000 genomes]
rs72996586	0.81[AMR][1000 genomes]
rs72998525	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs881217	0.86[CHB][hapmap];0.85[CHD][hapmap];0.91[JPT][hapmap];0.92[MEX][hapmap];0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs949069	0.90[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.84[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4944994	FCHSD2	cis	cerebellum	SCAN
rs4944994	PDE2A	cis	parietal	SCAN
rs4944994	XRRA1,RNF169	cis	occipital cortex	BrainEAC

Chromatin state (count:44 , 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	chr11:74864800-74870400	Enhancers	Fetal Intestine Large	intestine
4	chr11:74865000-74872000	Enhancers	Placenta	Placenta
5	chr11:74866200-74873000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr11:74866400-74870000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr11:74866400-74871000	Weak transcription	Spleen	Spleen
8	chr11:74866400-74873000	Weak transcription	Fetal Thymus	thymus
9	chr11:74866800-74870400	Weak transcription	Left Ventricle	heart
10	chr11:74867400-74870200	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr11:74867400-74870800	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr11:74867400-74870800	Weak transcription	A549	lung
13	chr11:74867400-74873200	Weak transcription	Brain Cingulate Gyrus	brain
14	chr11:74867600-74870000	Weak transcription	Right Ventricle	heart
15	chr11:74867600-74870200	Weak transcription	Adipose Nuclei	Adipose
16	chr11:74867600-74870400	Weak transcription	Rectal Smooth Muscle	rectum
17	chr11:74867600-74870400	Weak transcription	Right Atrium	heart
18	chr11:74867600-74870800	Weak transcription	Stomach Smooth Muscle	stomach
19	chr11:74867600-74875000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr11:74867800-74870000	Genic enhancers	Duodenum Mucosa	Duodenum
21	chr11:74867800-74870400	Enhancers	HepG2	liver
22	chr11:74868200-74870000	Enhancers	Liver	Liver
23	chr11:74868600-74870400	Weak transcription	Fetal Muscle Leg	muscle
24	chr11:74868600-74870800	Weak transcription	Fetal Stomach	stomach
25	chr11:74868600-74875200	Weak transcription	Ovary	ovary
26	chr11:74868800-74870000	Weak transcription	Small Intestine	intestine
27	chr11:74868800-74870600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr11:74869200-74870400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr11:74869400-74870200	Enhancers	Colonic Mucosa	Colon
30	chr11:74869400-74870400	Genic enhancers	Fetal Intestine Small	intestine
31	chr11:74869600-74870000	Enhancers	Skeletal Muscle Male	skeletal muscle
32	chr11:74869600-74870200	Enhancers	Rectal Mucosa Donor 31	rectum
33	chr11:74869600-74870400	Enhancers	Rectal Mucosa Donor 29	rectum
34	chr11:74869600-74871000	Enhancers	Stomach Mucosa	stomach
35	chr11:74869600-74871200	Genic enhancers	Lung	lung
36	chr11:74869600-74871400	Enhancers	Brain Anterior Caudate	brain
37	chr11:74869800-74870000	Enhancers	Placenta Amnion	Placenta Amnion
38	chr11:74869800-74870800	Weak transcription	Brain Substantia Nigra	brain
39	chr11:74869800-74871200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr11:74869800-74871200	Enhancers	Brain Hippocampus Middle	brain
41	chr11:74869800-74871600	Enhancers	Fetal Muscle Trunk	muscle
42	chr11:74869800-74871800	Enhancers	Gastric	stomach
43	chr11:74869800-74871800	Enhancers	Pancreas	Pancrea
44	chr11:74869800-74872200	Enhancers	Sigmoid Colon	Sigmoid Colon

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