Variant report

Variant	rs11731878
Chromosome Location	chr4:99950682-99950683
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr4:99950251-99950859	H1-neurons	neurons:	n/a	n/a
2	POLR2A	chr4:99950485-99950817	H1-neurons	neurons:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:99915586..99918527-chr4:99948157..99950795,3	MCF-7	breast:
2	chr4:99847981..99851053-chr4:99948406..99952030,4	K562	blood:
3	chr4:99913236..99916407-chr4:99949384..99951097,3	K562	blood:
4	chr4:99847981..99851053-chr4:99948406..99952184,4	K562	blood:
5	chr4:99848335..99851171-chr4:99949234..99951103,2	MCF-7	breast:
6	chr4:99936341..99939082-chr4:99948157..99950899,3	MCF-7	breast:

No data

Variant related genes	Relation type
METAP1	TF binding region
ENSG00000238449	Chromatin interaction
ENSG00000164024	Chromatin interaction
ENSG00000263923	Chromatin interaction
ENSG00000151247	Chromatin interaction

Extended variants
information (count: 72 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs10014193	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10016255	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10023577	0.85[CEU][hapmap]
rs10035037	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1037475	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10433890	0.85[CEU][hapmap]
rs11097643	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11097645	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11721765	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11723037	0.85[CEU][hapmap]
rs11725932	0.82[CEU][hapmap]
rs11730116	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11944824	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1230159	1.00[CHB][hapmap];0.95[ASN][1000 genomes]
rs1230160	0.95[ASN][1000 genomes]
rs1230169	0.95[ASN][1000 genomes]
rs1230174	0.90[ASN][1000 genomes]
rs1230175	1.00[CHB][hapmap];0.95[ASN][1000 genomes]
rs1230178	1.00[CHB][hapmap];0.95[ASN][1000 genomes]
rs1230179	1.00[CHB][hapmap];0.95[ASN][1000 genomes]
rs1230182	1.00[CHB][hapmap];0.95[ASN][1000 genomes]
rs1230186	1.00[CHB][hapmap];0.95[ASN][1000 genomes]
rs1230195	1.00[CHB][hapmap];0.95[ASN][1000 genomes]
rs1230196	0.90[CHB][hapmap];0.81[JPT][hapmap];0.95[ASN][1000 genomes]
rs1230197	0.95[ASN][1000 genomes]
rs1230200	0.95[ASN][1000 genomes]
rs1230203	0.88[ASN][1000 genomes]
rs1230205	0.92[CHB][hapmap];0.91[ASN][1000 genomes]
rs1230206	0.92[CHB][hapmap];0.91[ASN][1000 genomes]
rs1230207	0.91[ASN][1000 genomes]
rs1230209	1.00[CHB][hapmap];0.94[ASN][1000 genomes]
rs1234973	1.00[CHB][hapmap];0.95[ASN][1000 genomes]
rs12374261	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1238741	0.92[CHB][hapmap];0.91[ASN][1000 genomes]
rs12498533	0.84[CEU][hapmap]
rs12512420	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12644580	0.85[CEU][hapmap]
rs1453869	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1453871	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1584838	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17028293	0.81[CEU][hapmap]
rs17216446	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1869459	1.00[CEU][hapmap];0.86[CHB][hapmap];0.81[JPT][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2123782	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2167981	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2602910	1.00[CHB][hapmap];0.95[ASN][1000 genomes]
rs28539514	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2866032	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35203362	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3974876	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4699693	0.85[CEU][hapmap]
rs57098596	0.91[ASN][1000 genomes]
rs62323229	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6810489	0.81[CEU][hapmap]
rs6817991	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6822589	0.85[CEU][hapmap];0.82[ASN][1000 genomes]
rs6830125	0.85[CEU][hapmap]
rs6840282	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6840922	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6846221	0.96[CEU][hapmap];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6848246	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6850128	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6850293	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6852715	0.85[CEU][hapmap]
rs6854386	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7656935	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7674742	0.96[CEU][hapmap];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7676259	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7690818	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9685062	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9992105	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[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	nsv1009017	chr4:99669441-100406394	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:99931600-99971400	Weak transcription	Aorta	Aorta
2	chr4:99932600-99969800	Weak transcription	Skeletal Muscle Female	skeletal muscle
3	chr4:99937600-99966200	Weak transcription	HUVEC	blood vessel
4	chr4:99942200-99969600	Weak transcription	Fetal Brain Female	brain
5	chr4:99942600-99953400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr4:99942800-99955800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr4:99942800-99957000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr4:99943000-99951400	Weak transcription	HMEC	breast
9	chr4:99943000-99959200	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr4:99943600-99953400	Weak transcription	Primary hematopoietic stem cells	blood
11	chr4:99943800-99966200	Weak transcription	Adipose Nuclei	Adipose
12	chr4:99944200-99951000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr4:99944200-99966200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr4:99944200-99968800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr4:99944200-99969600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr4:99944200-99979000	Weak transcription	Colonic Mucosa	Colon
17	chr4:99944200-99979200	Weak transcription	Right Ventricle	heart
18	chr4:99944400-99950800	Weak transcription	NHLF	lung
19	chr4:99944400-99952800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
20	chr4:99944400-99955200	Weak transcription	NH-A	brain
21	chr4:99944400-99955400	Weak transcription	Primary monocytes fromperipheralblood	blood
22	chr4:99944400-99958400	Weak transcription	Fetal Muscle Trunk	muscle
23	chr4:99944400-99958800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr4:99944400-99958800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr4:99944400-99958800	Weak transcription	Fetal Muscle Leg	muscle
26	chr4:99944400-99959400	Weak transcription	HSMM	muscle
27	chr4:99944400-99965000	Weak transcription	Primary T cells fromperipheralblood	blood
28	chr4:99944400-99966400	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr4:99944400-99967200	Weak transcription	Fetal Stomach	stomach
30	chr4:99944400-99971600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr4:99944400-99979200	Weak transcription	Brain Hippocampus Middle	brain
32	chr4:99945000-99969600	Weak transcription	Rectal Smooth Muscle	rectum
33	chr4:99945600-99950800	Enhancers	Fetal Intestine Large	intestine
34	chr4:99945600-99951400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr4:99945600-99957000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr4:99946000-99976800	Weak transcription	Stomach Mucosa	stomach
37	chr4:99946200-99953600	Weak transcription	H9 Cell Line	embryonic stem cell
38	chr4:99946200-99970000	Weak transcription	Brain Anterior Caudate	brain
39	chr4:99946200-99977000	Weak transcription	Colon Smooth Muscle	Colon
40	chr4:99946400-99951000	Weak transcription	Fetal Thymus	thymus
41	chr4:99946400-99969000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
42	chr4:99946400-99969400	Weak transcription	Placenta	Placenta
43	chr4:99946400-99973600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr4:99946400-99979000	Weak transcription	Esophagus	oesophagus
45	chr4:99946600-99964800	Weak transcription	Duodenum Mucosa	Duodenum
46	chr4:99946600-99970000	Weak transcription	Hela-S3	cervix
47	chr4:99947000-99951600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
48	chr4:99947000-99953200	Weak transcription	H1 Cell Line	embryonic stem cell
49	chr4:99947000-99955200	Weak transcription	Cortex derived primary cultured neurospheres	brain
50	chr4:99947000-99955600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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