Variant report

Variant	rs4100076
Chromosome Location	chr11:74861416-74861417
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:74860426..74862138-chr11:74866873..74869626,2	K562	blood:
2	chr11:74860782..74862620-chr11:74866728..74869676,2	MCF-7	breast:
3	chr11:74860499..74862617-chr11:74862814..74864502,2	K562	blood:

Variant related genes	Relation type
ENSG00000137491	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10793114	0.83[AMR][1000 genomes]
rs10899076	0.86[CHB][hapmap];0.81[CHD][hapmap];0.80[GIH][hapmap];0.90[JPT][hapmap];0.88[MEX][hapmap];0.83[AMR][1000 genomes]
rs10899077	0.92[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs10899078	0.82[CHB][hapmap];0.85[CHD][hapmap];0.92[MEX][hapmap];0.92[AMR][1000 genomes]
rs10899079	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]
rs11236348	0.89[CHB][hapmap];0.88[JPT][hapmap];0.84[AMR][1000 genomes]
rs11236349	0.86[CHB][hapmap];0.90[JPT][hapmap];0.84[AMR][1000 genomes]
rs11236350	0.86[CHB][hapmap];0.81[CHD][hapmap];0.90[JPT][hapmap];0.88[MEX][hapmap];0.81[AMR][1000 genomes]
rs11236351	0.84[AMR][1000 genomes]
rs11236352	0.84[AMR][1000 genomes]
rs11236353	0.84[AMR][1000 genomes]
rs11236354	0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs11236356	1.00[CEU][hapmap];0.91[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.81[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11236357	0.82[CHB][hapmap];0.81[CHD][hapmap];0.84[MEX][hapmap];0.88[AMR][1000 genomes]
rs11236358	0.86[ASN][1000 genomes]
rs11236361	1.00[CEU][hapmap];0.86[CHB][hapmap];0.92[CHD][hapmap];0.90[GIH][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11822379	0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs11827488	0.92[CEU][hapmap];0.83[CHB][hapmap]
rs12361277	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17133732	0.88[CEU][hapmap];0.84[CHB][hapmap];0.88[JPT][hapmap];0.86[ASN][1000 genomes]
rs3740839	0.89[CEU][hapmap];0.86[CHB][hapmap];0.89[CHD][hapmap];0.87[MEX][hapmap];0.92[TSI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4397881	1.00[CEU][hapmap];0.91[CHB][hapmap];0.88[GIH][hapmap];0.82[LWK][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4944072	0.86[ASN][1000 genomes]
rs4944073	1.00[CEU][hapmap];0.86[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];0.81[JPT][hapmap];0.80[MKK][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4944074	0.80[AMR][1000 genomes]
rs4944974	0.89[CEU][hapmap];0.81[CHB][hapmap];0.84[JPT][hapmap];0.84[TSI][hapmap]
rs4944990	0.91[CHB][hapmap];0.90[JPT][hapmap];0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs4944991	0.91[CHB][hapmap];0.87[CHD][hapmap];0.80[GIH][hapmap];0.90[JPT][hapmap];0.92[MEX][hapmap];0.92[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs4944992	0.82[CHB][hapmap];0.85[CHD][hapmap];0.92[MEX][hapmap];0.92[AMR][1000 genomes]
rs4944993	0.81[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.81[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4944994	0.82[CHB][hapmap];0.80[MEX][hapmap];0.81[AMR][1000 genomes]
rs57073688	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs59633704	0.84[AMR][1000 genomes]
rs61117837	0.87[ASN][1000 genomes]
rs6592602	0.89[CEU][hapmap];0.85[CHB][hapmap];0.83[CHD][hapmap];0.90[JPT][hapmap];0.92[TSI][hapmap];0.81[ASN][1000 genomes]
rs66687047	0.86[ASN][1000 genomes]
rs67904312	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs67947132	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72996586	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72998525	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs881217	1.00[CEU][hapmap];0.86[CHB][hapmap];0.87[CHD][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs949069	0.83[CHD][hapmap]

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	nsv526053	chr11:74857436-74861545	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs4100076	KCTD21	cis	cerebellum	SCAN
rs4100076	BTAF1	trans	cerebellum	SCAN
rs4100076	PGM2L1	cis	cerebellum	SCAN
rs4100076	UVRAG	cis	parietal	SCAN
rs4100076	GDPD4	cis	cerebellum	SCAN
rs4100076	FCHSD2	cis	cerebellum	SCAN
rs4100076	NEU3	cis	cerebellum	SCAN

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:74852000-74861600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr11:74853800-74862000	Enhancers	HepG2	liver
3	chr11:74853800-74862200	Enhancers	Placenta	Placenta
4	chr11:74854000-74862000	Enhancers	Fetal Intestine Large	intestine
5	chr11:74855200-74862200	Enhancers	Fetal Intestine Small	intestine
6	chr11:74855600-74861600	Weak transcription	Brain Cingulate Gyrus	brain
7	chr11:74856600-74863400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr11:74857400-74865600	Weak transcription	Small Intestine	intestine
9	chr11:74859000-74862200	Weak transcription	Left Ventricle	heart
10	chr11:74859000-74862400	Weak transcription	Liver	Liver
11	chr11:74859000-74863800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr11:74859200-74861800	Weak transcription	Fetal Muscle Trunk	muscle
13	chr11:74859200-74862200	Weak transcription	Right Atrium	heart
14	chr11:74859200-74862400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr11:74859200-74863200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr11:74859400-74862200	Enhancers	Monocytes-CD14+_RO01746	blood
17	chr11:74859800-74862200	Weak transcription	Lung	lung
18	chr11:74860000-74864000	Weak transcription	Spleen	Spleen
19	chr11:74860400-74862000	Enhancers	Sigmoid Colon	Sigmoid Colon
20	chr11:74860600-74861600	Enhancers	Rectal Mucosa Donor 29	rectum
21	chr11:74860600-74862000	Enhancers	Rectal Mucosa Donor 31	rectum
22	chr11:74860600-74862200	Enhancers	Colonic Mucosa	Colon
23	chr11:74861000-74862200	Enhancers	Esophagus	oesophagus
24	chr11:74861000-74862200	Enhancers	Stomach Mucosa	stomach
25	chr11:74861000-74862400	Enhancers	Primary monocytes fromperipheralblood	blood
26	chr11:74861200-74861800	Enhancers	Skeletal Muscle Female	skeletal muscle
27	chr11:74861200-74862000	Enhancers	Fetal Muscle Leg	muscle
28	chr11:74861200-74862000	Enhancers	Fetal Thymus	thymus
29	chr11:74861200-74862000	Enhancers	Pancreas	Pancrea
30	chr11:74861200-74863600	Enhancers	Gastric	stomach
31	chr11:74861200-74868400	Active TSS	Brain Hippocampus Middle	brain
32	chr11:74861400-74862000	Enhancers	Adipose Nuclei	Adipose
33	chr11:74861400-74862000	Flanking Active TSS	Duodenum Mucosa	Duodenum
34	chr11:74861400-74862400	Enhancers	Fetal Stomach	stomach
35	chr11:74861400-74864000	Bivalent/Poised TSS	Stomach Smooth Muscle	stomach
36	chr11:74861400-74866000	Active TSS	Brain Anterior Caudate	brain

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