Variant report

Variant	rs11097645
Chromosome Location	chr4:99946126-99946127
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:23)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:23 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr4:99946100-99946250	Caco-2	colon:	n/a	n/a
2	CTCF	chr4:99946120-99946270	HEEpiC	esophagus:	n/a	n/a
3	RAD21	chr4:99946040-99946403	H1-hESC	embryonic stem cell:	n/a	n/a
4	RAD21	chr4:99946123-99946320	H1-hESC	embryonic stem cell:	n/a	n/a
5	CTCF	chr4:99946100-99946250	NHEK	skin:	n/a	n/a
6	CTCF	chr4:99946101-99946326	MCF-7	breast:	n/a	n/a
7	CTCF	chr4:99946000-99946150	NHEK	skin:	n/a	n/a
8	CTCF	chr4:99946080-99946230	RPTEC	kidney:	n/a	n/a
9	RAD21	chr4:99946045-99946338	MCF-7	breast:	n/a	n/a
10	CTCF	chr4:99946020-99946170	RPTEC	kidney:	n/a	n/a
11	CTCF	chr4:99946050-99946344	K562	blood:	n/a	n/a
12	CTCF	chr4:99946100-99946250	A549	lung:	n/a	n/a
13	MAZ	chr4:99946105-99946243	K562	blood:	n/a	n/a
14	RAD21	chr4:99945965-99946337	MCF-7	breast:	n/a	n/a
15	CTCF	chr4:99946119-99946303	MCF-7	breast:	n/a	n/a
16	CTCF	chr4:99946117-99946298	Pancreas_OC	pancreas:	n/a	n/a
17	CTCF	chr4:99946020-99946170	BE2_C	brain:	n/a	n/a
18	CTCF	chr4:99946060-99946319	K562	blood:	n/a	n/a
19	CTCF	chr4:99946051-99946309	K562	blood:	n/a	n/a
20	CTCF	chr4:99946109-99946276	HepG2	liver:	n/a	n/a
21	RAD21	chr4:99946069-99946297	K562	blood:	n/a	n/a
22	GATA1	chr4:99944563-99946168	K562	blood:	n/a	n/a
23	CTCF	chr4:99946098-99946295	Medullo	brain:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:99916503..99921369-chr4:99944985..99949729,5	K562	blood:
2	chr4:99937858..99939878-chr4:99945030..99946668,2	MCF-7	breast:
3	chr4:99945722..99947995-chr4:99951223..99953037,2	K562	blood:
4	chr4:99915571..99917761-chr4:99944476..99946805,2	K562	blood:

No data

Variant related genes	Relation type
ABT1P1	TF binding region
ENSG00000164024	Chromatin interaction
ENSG00000265213	Chromatin interaction

Extended variants
information (count: 81 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs10014193	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10016255	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10023577	0.85[CEU][hapmap]
rs10035037	0.84[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1037475	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10433890	0.85[CEU][hapmap]
rs11097643	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1154404	0.82[YRI][hapmap]
rs1154415	1.00[YRI][hapmap]
rs11721765	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11723037	0.84[CEU][hapmap]
rs11725932	0.81[CEU][hapmap]
rs11730116	0.89[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11731878	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]
rs11940529	0.81[EUR][1000 genomes]
rs11944824	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1230159	0.92[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	0.92[CHB][hapmap];0.95[ASN][1000 genomes]
rs1230178	0.92[CHB][hapmap];0.95[ASN][1000 genomes]
rs1230179	0.92[CHB][hapmap];0.95[ASN][1000 genomes]
rs1230182	0.92[CHB][hapmap];0.95[ASN][1000 genomes]
rs1230186	0.92[CHB][hapmap];0.95[ASN][1000 genomes]
rs1230195	0.92[CHB][hapmap];0.95[ASN][1000 genomes]
rs1230196	0.80[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	0.85[CHB][hapmap];0.91[ASN][1000 genomes]
rs1230206	0.85[CHB][hapmap];0.91[ASN][1000 genomes]
rs1230207	0.91[ASN][1000 genomes]
rs1230209	0.92[CHB][hapmap];0.94[ASN][1000 genomes]
rs1234973	0.92[CHB][hapmap];0.95[ASN][1000 genomes]
rs12374261	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1238741	0.85[CHB][hapmap];0.91[ASN][1000 genomes]
rs12498533	0.83[CEU][hapmap]
rs12512420	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12644580	0.85[CEU][hapmap]
rs1311621	0.85[YRI][hapmap]
rs13148577	0.82[YRI][hapmap]
rs1453869	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1453871	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1584838	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17216446	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17595102	1.00[YRI][hapmap]
rs1869458	1.00[YRI][hapmap]
rs1869459	1.00[CEU][hapmap];0.81[JPT][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2123782	0.84[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2167981	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2602910	0.92[CHB][hapmap];0.95[ASN][1000 genomes]
rs2851275	1.00[YRI][hapmap]
rs2851301	1.00[YRI][hapmap]
rs28539514	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2866032	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35203362	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3974876	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4699693	0.84[CEU][hapmap]
rs57098596	0.91[ASN][1000 genomes]
rs62323229	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6810489	0.80[CEU][hapmap]
rs6817991	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6822589	0.85[CEU][hapmap];0.82[ASN][1000 genomes]
rs6830125	0.84[CEU][hapmap]
rs6840282	0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6840922	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6846221	0.96[CEU][hapmap];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6848246	0.85[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6850128	0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6850293	0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6852715	0.84[CEU][hapmap]
rs6854386	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7656935	0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7674742	0.96[CEU][hapmap];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7676259	0.85[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7690818	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9685029	0.81[EUR][1000 genomes]
rs9685062	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9992105	0.97[AMR][1000 genomes];0.94[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:107 , 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	chr4:99942200-99950400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr4:99942200-99969600	Weak transcription	Fetal Brain Female	brain
6	chr4:99942600-99946800	Weak transcription	Psoas Muscle	Psoas
7	chr4:99942600-99950000	Weak transcription	Dnd41	blood
8	chr4:99942600-99953400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr4:99942800-99946200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr4:99942800-99946200	Weak transcription	Ovary	ovary
11	chr4:99942800-99948800	Weak transcription	NHDF-Ad	bronchial
12	chr4:99942800-99955800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr4:99942800-99957000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr4:99943000-99949600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr4:99943000-99951400	Weak transcription	HMEC	breast
16	chr4:99943000-99959200	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr4:99943200-99949400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr4:99943200-99950600	Weak transcription	Primary B cells from peripheral blood	blood
19	chr4:99943400-99947000	Enhancers	Pancreas	Pancrea
20	chr4:99943400-99950600	Weak transcription	Monocytes-CD14+_RO01746	blood
21	chr4:99943600-99947000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
22	chr4:99943600-99947400	Enhancers	Primary T helper cells PMA-I stimulated	--
23	chr4:99943600-99953400	Weak transcription	Primary hematopoietic stem cells	blood
24	chr4:99943800-99946200	Enhancers	H9 Cell Line	embryonic stem cell
25	chr4:99943800-99966200	Weak transcription	Adipose Nuclei	Adipose
26	chr4:99944000-99946400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr4:99944000-99947000	Enhancers	iPS-20b Cell Line	embryonic stem cell
28	chr4:99944000-99948000	Enhancers	Breast Myoepithelial Primary Cells	Breast
29	chr4:99944200-99946200	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr4:99944200-99946400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr4:99944200-99946600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
32	chr4:99944200-99947000	Enhancers	iPS-18 Cell Line	embryonic stem cell
33	chr4:99944200-99947000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
34	chr4:99944200-99949400	Weak transcription	Right Atrium	heart
35	chr4:99944200-99949800	Weak transcription	Primary T cells from cord blood	blood
36	chr4:99944200-99950600	Weak transcription	Primary B cells from cord blood	blood
37	chr4:99944200-99951000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr4:99944200-99966200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr4:99944200-99968800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr4:99944200-99969600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr4:99944200-99979000	Weak transcription	Colonic Mucosa	Colon
42	chr4:99944200-99979200	Weak transcription	Right Ventricle	heart
43	chr4:99944400-99946600	Enhancers	HUES64 Cell Line	embryonic stem cell
44	chr4:99944400-99948400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr4:99944400-99948600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr4:99944400-99948600	Weak transcription	Thymus	Thymus
47	chr4:99944400-99949400	Weak transcription	GM12878-XiMat	blood
48	chr4:99944400-99949600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr4:99944400-99949600	Enhancers	Fetal Intestine Small	intestine
50	chr4:99944400-99950200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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