Variant report

Variant	rs3762002
Chromosome Location	chr6:143823157-143823158
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:64)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:64 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr6:143823080-143823230	HAc	cerebellar:	n/a	n/a
2	CTCF	chr6:143823147-143823198	GM19238	blood:	n/a	n/a
3	CTCF	chr6:143823107-143823241	NHEK	skin:	n/a	n/a
4	RAD21	chr6:143822992-143823267	SK-N-SH_RA	brain:	n/a	n/a
5	CTCF	chr6:143823100-143823250	WERI-Rb-1	eye:	n/a	n/a
6	CTCF	chr6:143823117-143823214	GM12892	blood:	n/a	n/a
7	CTCF	chr6:143823120-143823270	HRPEpiC	eye:	n/a	n/a
8	CTCF	chr6:143823132-143823239	MCF-7	breast:	n/a	n/a
9	CTCF	chr6:143823128-143823218	A549	lung:	n/a	n/a
10	CTCF	chr6:143823140-143823290	HPAF	blood vessel:	n/a	n/a
11	CTCF	chr6:143823104-143823256	MCF-7	breast:	n/a	n/a
12	CTCF	chr6:143823098-143823284	LNCaP	prostate:	n/a	n/a
13	CTCF	chr6:143823060-143823210	HPAF	blood vessel:	n/a	n/a
14	CTCF	chr6:143823140-143823290	Hela-S3	cervix:	n/a	n/a
15	CTCF	chr6:143823120-143823270	HCPEpiC	choroid plexus:	n/a	n/a
16	CTCF	chr6:143823120-143823270	HMEC	breast:	n/a	n/a
17	RAD21	chr6:143822970-143823374	MCF-7	breast:	n/a	n/a
18	CTCF	chr6:143823091-143823348	K562	blood:	n/a	n/a
19	RAD21	chr6:143823083-143823248	IMR90	lung:	n/a	n/a
20	CTCF	chr6:143823100-143823250	HMEC	breast:	n/a	n/a
21	CTCF	chr6:143823040-143823190	GM06990	blood:	n/a	n/a
22	CTCF	chr6:143823157-143823240	K562	blood:	n/a	n/a
23	CTCF	chr6:143823040-143823190	AG04450	lung:	n/a	n/a
24	CTCF	chr6:143823140-143823290	HPF	lung:	n/a	n/a
25	CTCF	chr6:143823120-143823270	AG09309	skin:	n/a	n/a
26	CTCF	chr6:143823100-143823250	AG09319	gingival:	n/a	n/a
27	CTCF	chr6:143823120-143823270	HA-sp	spinal cord:	n/a	n/a
28	CTCF	chr6:143823130-143823248	Hela-S3	cervix:	n/a	n/a
29	RAD21	chr6:143822977-143823330	HepG2	liver:	n/a	n/a
30	CTCF	chr6:143823120-143823270	AG04449	skin:	n/a	n/a
31	RAD21	chr6:143823107-143823356	A549	lung:	n/a	n/a
32	CTCF	chr6:143823020-143823170	HFF	foreskin:	n/a	n/a
33	RAD21	chr6:143822848-143823486	SK-N-SH	brain:	n/a	n/a
34	RAD21	chr6:143823057-143823314	Hela-S3	cervix:	n/a	n/a
35	CTCF	chr6:143823124-143823244	GM19240	blood:	n/a	n/a
36	CTCF	chr6:143823088-143823244	HepG2	liver:	n/a	n/a
37	CTCF	chr6:143823077-143823299	IMR90	lung:	n/a	n/a
38	CTCF	chr6:143823100-143823250	AG04450	lung:	n/a	n/a
39	CTCF	chr6:143823091-143823312	Medullo	brain:	n/a	n/a
40	RAD21	chr6:143823063-143823249	HepG2	liver:	n/a	n/a
41	RAD21	chr6:143823046-143823371	H1-hESC	embryonic stem cell:	n/a	n/a
42	CTCF	chr6:143823120-143823270	AG10803	skin:	n/a	n/a
43	RAD21	chr6:143822949-143823408	HCT-116	colon:	n/a	n/a
44	CTCF	chr6:143823152-143823226	Fibrobl	skin:	n/a	n/a
45	CTCF	chr6:143823100-143823250	A549	lung:	n/a	n/a
46	ZNF143	chr6:143823119-143823254	GM12878	blood:	n/a	n/a
47	CTCF	chr6:143823130-143823274	LNCaP	prostate:	n/a	n/a
48	CTCF	chr6:143823130-143823227	HepG2	liver:	n/a	n/a
49	CTCF	chr6:143823100-143823250	GM12878	blood:	n/a	n/a
50	CTCF	chr6:143823100-143823250	AG10803	skin:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:143821189..143823852-chr6:143831025..143833660,2	MCF-7	breast:
2	chr6:143810260..143812960-chr6:143821812..143824158,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000229036	TF binding region
ENSG00000241847	Chromatin interaction
ENSG00000001036	Chromatin interaction
ENSG00000229036	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs1061220	0.87[JPT][hapmap]
rs1065355	0.82[CEU][hapmap];0.82[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.80[TSI][hapmap];0.87[EUR][1000 genomes]
rs10782288	0.88[EUR][1000 genomes]
rs10782289	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10809	0.81[CEU][hapmap];0.92[CHB][hapmap];0.90[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12196227	0.82[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs12199192	0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1338533	0.90[EUR][1000 genomes]
rs1424922	0.94[CEU][hapmap];0.86[EUR][1000 genomes]
rs1978529	0.93[EUR][1000 genomes]
rs2143137	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2272924	0.83[CEU][hapmap];0.87[JPT][hapmap]
rs2294505	0.94[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2294506	0.94[CEU][hapmap];0.97[TSI][hapmap]
rs2496593	0.82[JPT][hapmap]
rs3088203	0.87[JPT][hapmap]
rs3761999	0.81[JPT][hapmap]
rs3762000	0.87[CEU][hapmap];0.88[EUR][1000 genomes]
rs3762001	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3789789	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3789790	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][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]
rs3789791	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3804538	0.94[CEU][hapmap];0.82[CHB][hapmap];0.83[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3804539	0.94[CEU][hapmap];0.82[CHB][hapmap];0.83[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3804544	0.83[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4895612	0.81[JPT][hapmap]
rs4895614	0.81[JPT][hapmap]
rs4895615	0.94[CEU][hapmap];0.89[EUR][1000 genomes]
rs4896656	0.81[JPT][hapmap]
rs4896659	0.87[EUR][1000 genomes]
rs4896660	0.94[CEU][hapmap];0.88[EUR][1000 genomes]
rs6924268	0.88[EUR][1000 genomes]
rs6926733	0.94[CEU][hapmap];0.86[EUR][1000 genomes]
rs6929191	0.81[JPT][hapmap]
rs6930325	0.94[CEU][hapmap];0.89[EUR][1000 genomes]
rs6935346	0.94[CEU][hapmap];0.97[TSI][hapmap];0.89[EUR][1000 genomes]
rs6935618	0.94[CEU][hapmap];0.87[JPT][hapmap];0.86[EUR][1000 genomes]
rs7741976	0.94[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7751011	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9321913	0.83[CEU][hapmap];0.82[CHB][hapmap];0.86[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs9321914	0.94[CEU][hapmap];0.94[TSI][hapmap];0.88[EUR][1000 genomes]
rs9373391	0.81[JPT][hapmap]
rs9373393	0.94[CEU][hapmap];0.97[TSI][hapmap];0.88[EUR][1000 genomes]
rs9376750	0.83[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs9376753	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9390092	0.81[JPT][hapmap]
rs9390094	0.94[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9390096	1.00[CEU][hapmap];0.86[CHD][hapmap];0.87[GIH][hapmap];0.90[MEX][hapmap];0.88[EUR][1000 genomes]
rs9399442	0.86[EUR][1000 genomes]
rs9399443	0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9403492	0.87[EUR][1000 genomes]
rs9403494	0.94[CEU][hapmap];0.92[CHB][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9403496	0.94[CEU][hapmap];0.92[CHB][hapmap];0.90[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];0.93[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	esv2757193	chr6:143820009-143825104	Strong transcription Weak transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	esv2759475	chr6:143820009-143825104	Weak transcription Strong transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3762002	FUCA2	cis	parietal	SCAN
rs3762002	HIVEP2	cis	parietal	SCAN
rs3762002	RAB32	cis	parietal	SCAN
rs3762002	PEX3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:143772600-143832000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr6:143773200-143827000	Weak transcription	Brain Germinal Matrix	brain
3	chr6:143773400-143832000	Weak transcription	Fetal Brain Male	brain
4	chr6:143781000-143832000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr6:143790200-143831600	Weak transcription	Esophagus	oesophagus
6	chr6:143790200-143831600	Weak transcription	Gastric	stomach
7	chr6:143795200-143827400	Weak transcription	Aorta	Aorta
8	chr6:143795800-143831800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr6:143797000-143826600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr6:143797600-143831000	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr6:143799000-143827000	Weak transcription	Brain Cingulate Gyrus	brain
12	chr6:143800800-143831000	Weak transcription	Colon Smooth Muscle	Colon
13	chr6:143805200-143827800	Weak transcription	Fetal Heart	heart
14	chr6:143811400-143832000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr6:143811800-143829400	Strong transcription	Monocytes-CD14+_RO01746	blood
16	chr6:143812000-143827400	Weak transcription	Pancreas	Pancrea
17	chr6:143812200-143831600	Weak transcription	Right Ventricle	heart
18	chr6:143812400-143826800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr6:143812400-143829600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr6:143812400-143832200	Weak transcription	Spleen	Spleen
21	chr6:143812600-143831800	Weak transcription	NHEK	skin
22	chr6:143812600-143832000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr6:143813000-143826600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr6:143813400-143828400	Strong transcription	Duodenum Mucosa	Duodenum
25	chr6:143813400-143829600	Strong transcription	Fetal Intestine Large	intestine
26	chr6:143813800-143828400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr6:143814200-143825600	Strong transcription	Fetal Muscle Trunk	muscle
28	chr6:143814200-143828200	Strong transcription	HSMM	muscle
29	chr6:143814200-143828800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr6:143814200-143829600	Strong transcription	K562	blood
31	chr6:143814400-143825600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
32	chr6:143814400-143830200	Strong transcription	Primary monocytes fromperipheralblood	blood
33	chr6:143814600-143823800	Strong transcription	Stomach Smooth Muscle	stomach
34	chr6:143814600-143828200	Strong transcription	HepG2	liver
35	chr6:143814600-143828600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr6:143814600-143831000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr6:143814800-143825400	Strong transcription	HUES48 Cell Line	embryonic stem cell
38	chr6:143814800-143825400	Strong transcription	Primary neutrophils fromperipheralblood	blood
39	chr6:143814800-143827200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr6:143814800-143828200	Strong transcription	Left Ventricle	heart
41	chr6:143814800-143828200	Strong transcription	NHLF	lung
42	chr6:143814800-143828400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr6:143814800-143828400	Strong transcription	Adipose Nuclei	Adipose
44	chr6:143814800-143829000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr6:143814800-143829200	Strong transcription	Rectal Mucosa Donor 29	rectum
46	chr6:143814800-143829400	Strong transcription	HUES64 Cell Line	embryonic stem cell
47	chr6:143814800-143831400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr6:143815000-143826000	Strong transcription	Duodenum Smooth Muscle	Duodenum
49	chr6:143815000-143828400	Strong transcription	HUES6 Cell Line	embryonic stem cell
50	chr6:143815000-143829000	Strong transcription	Liver	Liver

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