Variant report

Variant	rs5762803
Chromosome Location	chr22:29193638-29193639
allele	C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:18)
CpG islands
(count:0)
Chromatin interactive
region (count:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:18 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr22:29189733-29194459	GM18526	blood:	n/a	n/a
2	POLR2A	chr22:29189651-29193756	GM12878	blood:	n/a	n/a
3	POLR2A	chr22:29188106-29198866	HepG2	liver:	n/a	n/a
4	POLR2A	chr22:29188141-29193821	HepG2	liver:	n/a	n/a
5	POLR2A	chr22:29192908-29193797	ProgFib	skin:	n/a	n/a
6	POLR2A	chr22:29192300-29197471	MCF10A-Er-Src	breast:	n/a	n/a
7	POLR2A	chr22:29188193-29193681	GM19099	blood:	n/a	n/a
8	POLR2A	chr22:29188548-29193679	GM18951	blood:	n/a	n/a
9	HEY1	chr22:29193555-29193705	HepG2	liver:	n/a	n/a
10	POLR2A	chr22:29192244-29193650	H1-hESC	embryonic stem cell:	n/a	n/a
11	POLR2A	chr22:29186949-29198998	MCF-7	breast:	n/a	n/a
12	POLR2A	chr22:29193265-29193765	GM12892	blood:	n/a	n/a
13	HEY1	chr22:29188733-29193760	HepG2	liver:	n/a	chr22:29193424-29193433
14	POLR2A	chr22:29187961-29193653	GM12891	blood:	n/a	n/a
15	POLR2A	chr22:29189600-29193715	HepG2	liver:	n/a	n/a
16	POLR2A	chr22:29193531-29193711	HepG2	liver:	n/a	n/a
17	POLR2A	chr22:29187995-29198706	GM12878	blood:	n/a	n/a
18	POLR2A	chr22:29192364-29193754	GM12878	blood:	n/a	n/a

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr22:29193059..29194942-chr9:140134629..140136835,2	MCF-7	breast:
2	chr11:64644723..64647211-chr22:29193469..29195645,2	MCF-7	breast:
3	chr22:29127658..29141630-chr22:29187451..29201381,67	MCF-7	breast:
4	chr22:29134319..29139472-chr22:29186598..29194420,8	K562	blood:
5	chr22:29118802..29121164-chr22:29193533..29196083,2	MCF-7	breast:
6	chr22:29192790..29195000-chr8:144819981..144823300,3	MCF-7	breast:
7	chr22:28994240..28996811-chr22:29193296..29195303,2	MCF-7	breast:
8	chr22:29193615..29196363-chr22:29210020..29212072,3	K562	blood:
9	chr12:99739936..99741619-chr22:29193076..29195936,2	MCF-7	breast:
10	chr22:29165808..29174203-chr22:29186827..29200037,34	MCF-7	breast:
11	chr22:29134224..29141746-chr22:29191206..29200044,27	MCF-7	breast:
12	chr22:29166664..29171376-chr22:29189061..29194611,6	MCF-7	breast:
13	chr22:29191314..29194018-chr6:26240540..26242629,2	MCF-7	breast:
14	chr22:29193593..29195791-chr22:29251610..29254228,2	MCF-7	breast:

No data

Variant related genes	Relation type
XBP1	TF binding region
ENSG00000226471	TF binding region
ENSG00000272858	Chromatin interaction
ENSG00000110047	Chromatin interaction
ENSG00000188229	Chromatin interaction
ENSG00000198327	Chromatin interaction
ENSG00000203499	Chromatin interaction
ENSG00000100209	Chromatin interaction
ENSG00000183765	Chromatin interaction
ENSG00000159873	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs12628211	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2097461	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2239815	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2269577	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2347447	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2881635	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs35259224	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs3788409	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs5752795	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5752798	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5752801	0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs5752804	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs5752807	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs5752809	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs5752812	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs5752813	0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs5762784	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5762788	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs5762795	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5762815	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs5762824	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs5762825	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs5762853	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs5762854	0.83[ASN][1000 genomes]
rs5762863	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs5762864	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs5762867	0.80[ASN][1000 genomes]
rs5997408	0.83[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs6005867	0.84[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs6005869	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs6005872	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6005881	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6005892	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6005915	0.81[AMR][1000 genomes]
rs6005916	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6005927	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6005929	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7287124	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7287806	0.83[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs763073	0.80[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs8137969	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs9625566	0.94[ASN][1000 genomes]
rs9625588	0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916473	chr22:28837041-29215603	Weak transcription Bivalent Enhancer Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
2	nsv1064079	chr22:29065528-29456059	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
3	nsv834169	chr22:29095446-29303929	Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs5762803	CCDC117	Cis_1M	lymphoblastoid	RTeQTL
rs5762803	XBP1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:29170000-29194200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr22:29188200-29194200	Strong transcription	Brain Cingulate Gyrus	brain
3	chr22:29188400-29194200	Strong transcription	Fetal Stomach	stomach
4	chr22:29188600-29194400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr22:29188800-29194000	Strong transcription	Fetal Muscle Leg	muscle
6	chr22:29188800-29194200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr22:29188800-29194200	Strong transcription	Fetal Muscle Trunk	muscle
8	chr22:29189000-29194200	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
9	chr22:29189000-29195000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr22:29189200-29193800	Genic enhancers	Primary T killer naive cells fromperipheralblood	blood
11	chr22:29189200-29194000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr22:29189200-29194000	Genic enhancers	Primary T helper cells fromperipheralblood	blood
13	chr22:29189200-29194000	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
14	chr22:29189200-29194000	Strong transcription	Muscle Satellite Cultured Cells	--
15	chr22:29189800-29194000	Strong transcription	HUES6 Cell Line	embryonic stem cell
16	chr22:29189800-29194000	Strong transcription	Fetal Lung	lung
17	chr22:29189800-29194000	Strong transcription	HMEC	breast
18	chr22:29189800-29194000	Strong transcription	NHDF-Ad	bronchial
19	chr22:29189800-29194200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr22:29189800-29194600	Strong transcription	HUES48 Cell Line	embryonic stem cell
21	chr22:29189800-29194800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
22	chr22:29190000-29193800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr22:29190000-29194000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr22:29190000-29194000	Strong transcription	Cortex derived primary cultured neurospheres	brain
25	chr22:29190000-29194200	Strong transcription	H1 Cell Line	embryonic stem cell
26	chr22:29190000-29194200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
27	chr22:29190000-29194200	Genic enhancers	Primary T helper memory cells from peripheral blood 1	blood
28	chr22:29190000-29194400	Strong transcription	ES-I3 Cell Line	embryonic stem cell
29	chr22:29190000-29194400	Genic enhancers	Primary T killer memory cells from peripheral blood	blood
30	chr22:29190000-29194600	Strong transcription	HUES64 Cell Line	embryonic stem cell
31	chr22:29190200-29193800	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
32	chr22:29190200-29194000	Genic enhancers	K562	blood
33	chr22:29190200-29194200	Genic enhancers	Fetal Heart	heart
34	chr22:29190200-29194400	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
35	chr22:29190200-29195800	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr22:29190200-29196200	Transcr. at gene 5' and 3'	Dnd41	blood
37	chr22:29190400-29193800	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
38	chr22:29190400-29194200	Strong transcription	iPS-15b Cell Line	embryonic stem cell
39	chr22:29190600-29194000	Genic enhancers	Fetal Intestine Small	intestine
40	chr22:29190600-29194200	Strong transcription	Brain Germinal Matrix	brain
41	chr22:29191200-29194000	Genic enhancers	Primary T cells fromperipheralblood	blood
42	chr22:29191200-29194600	Genic enhancers	Left Ventricle	heart
43	chr22:29191200-29195000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr22:29191200-29195600	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells short term culture	blood
45	chr22:29191400-29194000	Genic enhancers	Placenta	Placenta
46	chr22:29191400-29194200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr22:29191400-29194400	Strong transcription	Esophagus	oesophagus
48	chr22:29191400-29194600	Genic enhancers	Adipose Nuclei	Adipose
49	chr22:29191400-29195800	Transcr. at gene 5' and 3'	Liver	Liver
50	chr22:29191600-29194000	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

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