Variant report

Variant	rs1044158
Chromosome Location	chr2:85826132-85826133
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:16)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:16 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:85825703-85830272	K562	blood:	n/a	n/a
2	POLR2A	chr2:85825162-85830624	HepG2	liver:	n/a	n/a
3	POLR2A	chr2:85825980-85826609	PANC-1	pancreas:	n/a	n/a
4	POLR2A	chr2:85825892-85830647	HepG2	liver:	n/a	n/a
5	POLR2A	chr2:85826113-85827512	GM12891	blood:	n/a	n/a
6	POLR2A	chr2:85826121-85826174	HUVEC	blood vessel:	n/a	n/a
7	POLR2A	chr2:85825695-85830271	K562	blood:	n/a	n/a
8	POLR2A	chr2:85825646-85827771	K562	blood:	n/a	n/a
9	HEY1	chr2:85825187-85827776	HepG2	liver:	n/a	n/a
10	POLR2A	chr2:85825540-85828209	K562	blood:	n/a	n/a
11	POLR2A	chr2:85825877-85830216	GM12878	blood:	n/a	n/a
12	POLR2A	chr2:85825695-85826213	HepG2	liver:	n/a	n/a
13	POLR2A	chr2:85825881-85827633	GM12878	blood:	n/a	n/a
14	POLR2A	chr2:85825324-85830119	K562	blood:	n/a	n/a
15	POLR2A	chr2:85825709-85827553	HepG2	liver:	n/a	n/a
16	POLR2A	chr2:85821285-85828013	HepG2	liver:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:85802926..85807956-chr2:85820760..85828546,8	K562	blood:
2	chr2:85764595..85768669-chr2:85824476..85831716,9	MCF-7	breast:
3	chr2:85785429..85790468-chr2:85820934..85826927,9	MCF-7	breast:
4	chr2:85764454..85770994-chr2:85819148..85831427,14	K562	blood:
5	chr2:85764018..85768553-chr2:85822883..85829718,12	MCF-7	breast:
6	chr2:85765237..85769549-chr2:85821409..85826975,10	K562	blood:
7	chr2:85782564..85785342-chr2:85825387..85826998,2	MCF-7	breast:

No data

Variant related genes	Relation type
USP39	TF binding region
ENSG00000115486	Chromatin interaction
ENSG00000118640	Chromatin interaction
ENSG00000168906	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10180770	0.81[CHB][hapmap]
rs10182351	0.80[CHB][hapmap]
rs10206961	0.87[GIH][hapmap]
rs1124836	0.81[CHB][hapmap];0.81[CHD][hapmap]
rs12463933	0.85[CEU][hapmap];0.91[TSI][hapmap];0.82[EUR][1000 genomes]
rs13383605	0.81[CHB][hapmap];0.82[CHD][hapmap]
rs13406807	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs14242	0.81[CHD][hapmap]
rs1562322	0.81[CHD][hapmap]
rs2040349	0.96[CEU][hapmap];0.95[GIH][hapmap];0.86[MEX][hapmap];0.98[TSI][hapmap];0.82[EUR][1000 genomes]
rs2118177	0.96[CEU][hapmap];0.95[GIH][hapmap];0.86[MEX][hapmap];0.98[TSI][hapmap];0.82[EUR][1000 genomes]
rs2232745	0.81[CHB][hapmap];0.84[CHD][hapmap]
rs2232747	0.81[CHB][hapmap]
rs2232748	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2232750	0.81[CHB][hapmap];0.84[CHD][hapmap]
rs2304564	0.81[CHB][hapmap];0.82[CHD][hapmap]
rs3821020	0.82[CHD][hapmap]
rs3827550	0.81[CHB][hapmap]
rs58588820	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62166774	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6547629	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6643	0.81[CHB][hapmap];0.84[CHD][hapmap]
rs6733550	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6743051	0.81[CHB][hapmap];0.82[CHD][hapmap]
rs9678632	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9752	0.83[EUR][1000 genomes]

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1044158	GGCX	cis	parietal	SCAN
rs1044158	VAMP8	cis	lymphoblastoid	seeQTL
rs1044158	GGCX	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:85823200-85829200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr2:85823600-85829000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr2:85823800-85828800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr2:85824000-85826200	Genic enhancers	Fetal Intestine Large	intestine
5	chr2:85824000-85826200	Genic enhancers	Fetal Thymus	thymus
6	chr2:85824000-85826600	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr2:85824000-85826800	Strong transcription	HUES48 Cell Line	embryonic stem cell
8	chr2:85824000-85826800	Strong transcription	Fetal Lung	lung
9	chr2:85824000-85826800	Strong transcription	Left Ventricle	heart
10	chr2:85824000-85827000	Strong transcription	H9 Cell Line	embryonic stem cell
11	chr2:85824000-85827000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr2:85824000-85827600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr2:85824000-85827600	Strong transcription	Aorta	Aorta
14	chr2:85824000-85828200	Genic enhancers	Liver	Liver
15	chr2:85824000-85828400	Genic enhancers	Skeletal Muscle Male	skeletal muscle
16	chr2:85824000-85828600	Strong transcription	HUES6 Cell Line	embryonic stem cell
17	chr2:85824000-85828600	Genic enhancers	Fetal Intestine Small	intestine
18	chr2:85824000-85828800	Weak transcription	Psoas Muscle	Psoas
19	chr2:85824200-85826400	Strong transcription	A549	lung
20	chr2:85824200-85826600	Strong transcription	NHEK	skin
21	chr2:85824200-85826800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
22	chr2:85824200-85826800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
23	chr2:85824200-85827000	Strong transcription	HUES64 Cell Line	embryonic stem cell
24	chr2:85824200-85827200	Strong transcription	H1 Cell Line	embryonic stem cell
25	chr2:85824200-85827200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr2:85824200-85827200	Strong transcription	Primary T cells from cord blood	blood
27	chr2:85824200-85827200	Strong transcription	Brain Anterior Caudate	brain
28	chr2:85824200-85827400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr2:85824200-85828200	Strong transcription	Fetal Brain Female	brain
30	chr2:85824200-85828400	Strong transcription	Cortex derived primary cultured neurospheres	brain
31	chr2:85824200-85828400	Weak transcription	Right Atrium	heart
32	chr2:85824200-85828600	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
33	chr2:85824200-85828600	Genic enhancers	Pancreas	Pancrea
34	chr2:85824400-85826400	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr2:85824400-85826400	Strong transcription	Esophagus	oesophagus
36	chr2:85824400-85826600	Strong transcription	Fetal Muscle Trunk	muscle
37	chr2:85824400-85826600	Strong transcription	Rectal Mucosa Donor 31	rectum
38	chr2:85824400-85826800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr2:85824400-85827000	Strong transcription	Osteobl	bone
40	chr2:85824400-85827200	Strong transcription	Primary neutrophils fromperipheralblood	blood
41	chr2:85824400-85827200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr2:85824400-85827200	Strong transcription	Muscle Satellite Cultured Cells	--
43	chr2:85824400-85827200	Strong transcription	Brain Hippocampus Middle	brain
44	chr2:85824400-85827200	Strong transcription	Rectal Mucosa Donor 29	rectum
45	chr2:85824400-85827200	Strong transcription	Monocytes-CD14+_RO01746	blood
46	chr2:85824400-85827400	Strong transcription	Primary monocytes fromperipheralblood	blood
47	chr2:85824400-85827400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr2:85824400-85827600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr2:85824400-85827800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr2:85824400-85828200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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