Variant report

Variant	rs7556716
Chromosome Location	chr2:191398003-191398004
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:13)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:13 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CHD1	chr2:191397854-191400364	GM12878	blood:	n/a	n/a
2	ZNF143	chr2:191397925-191398220	GM12878	blood:	n/a	n/a
3	RCOR1	chr2:191397909-191398294	K562	blood:	n/a	n/a
4	POLR2A	chr2:191397873-191400077	GM12878	blood:	n/a	n/a
5	SETDB1	chr2:191397984-191398285	U2OS	brain:	n/a	n/a
6	CBX3	chr2:191397864-191398305	K562	blood:	n/a	n/a
7	RCOR1	chr2:191397757-191398290	GM12878	blood:	n/a	n/a
8	RCOR1	chr2:191397897-191398477	K562	blood:	n/a	n/a
9	POLR2A	chr2:191397202-191400008	GM12878	blood:	n/a	n/a
10	MTA3	chr2:191397701-191400798	GM12878	blood:	n/a	n/a
11	ZNF143	chr2:191397997-191398222	K562	blood:	n/a	n/a
12	RCOR1	chr2:191397990-191398218	Hela-S3	cervix:	n/a	n/a
13	POLR2A	chr2:191397141-191400056	GM12891	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr2:191397602..191400323-chr2:191511853..191515845,7	MCF-7	breast:
2	chr2:191396816..191398352-chr2:191428817..191431655,2	K562	blood:
3	chr2:191397324..191399612-chr2:191415383..191418342,2	MCF-7	breast:
4	chr2:191397736..191401145-chr2:191512338..191515436,3	K562	blood:
5	chr2:191385869..191388991-chr2:191394619..191398567,3	K562	blood:
6	chr2:191389345..191393382-chr2:191397304..191400533,4	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000233654	TF binding region
ENSG00000251935	Chromatin interaction
ENSG00000138386	Chromatin interaction
ENSG00000189362	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10169169	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10171376	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10173975	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10179262	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10185147	0.94[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10185228	0.84[EUR][1000 genomes]
rs10189140	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10202274	0.97[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10204342	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10208737	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10209340	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10211375	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10737936	0.83[CEU][hapmap];0.82[CHB][hapmap];0.84[EUR][1000 genomes]
rs11553601	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11695439	1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs13031452	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13384743	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13386210	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13388162	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13395233	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13398741	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13405215	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13410179	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13412663	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13412823	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13412835	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13412879	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13417310	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13418943	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13421959	1.00[YRI][hapmap]
rs13429315	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1837686	0.87[ASN][1000 genomes]
rs3811608	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4283453	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4853712	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4853719	0.84[EUR][1000 genomes]
rs56715527	0.84[ASN][1000 genomes]
rs58210597	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58253207	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58433478	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs58708643	0.87[ASN][1000 genomes]
rs6434401	0.83[CEU][hapmap];0.82[CHB][hapmap];0.84[EUR][1000 genomes]
rs6706036	0.84[EUR][1000 genomes]
rs6711561	0.84[EUR][1000 genomes]
rs6717050	0.97[ASN][1000 genomes]
rs6741118	0.84[EUR][1000 genomes]
rs72903349	0.82[ASN][1000 genomes]
rs72903383	0.86[ASN][1000 genomes]
rs72905242	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73054092	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7560045	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7562013	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7564107	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7574844	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7584379	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7594994	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7609330	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs894072	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs8962	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs9288174	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9967829	0.83[CEU][hapmap];0.82[CHB][hapmap];0.84[EUR][1000 genomes]

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7556716	FLJ20160	Cis_1M	lymphoblastoid	RTeQTL
rs7556716	NAB1	Cis_1M	lymphoblastoid	RTeQTL
rs7556716	FLJ20160	cis	multi-tissue	Pritchard

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:191357200-191398200	Weak transcription	Fetal Kidney	kidney
2	chr2:191362800-191398200	Weak transcription	Fetal Brain Male	brain
3	chr2:191375200-191398600	Weak transcription	Ovary	ovary
4	chr2:191379400-191398200	Weak transcription	Stomach Smooth Muscle	stomach
5	chr2:191382600-191398400	Weak transcription	Psoas Muscle	Psoas
6	chr2:191387400-191398600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr2:191391200-191398400	Weak transcription	Small Intestine	intestine
8	chr2:191391200-191398600	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr2:191393200-191398200	Enhancers	Primary hematopoietic stem cells	blood
10	chr2:191393200-191398600	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr2:191393400-191398600	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr2:191393400-191398600	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr2:191393400-191398600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr2:191393600-191398400	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr2:191393600-191398600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr2:191393800-191398400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr2:191394000-191398200	Enhancers	Fetal Lung	lung
18	chr2:191394200-191398200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
19	chr2:191394600-191398200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
20	chr2:191394600-191398200	Enhancers	NHEK	skin
21	chr2:191394800-191398200	Weak transcription	Primary neutrophils fromperipheralblood	blood
22	chr2:191394800-191398200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr2:191394800-191398400	Weak transcription	Fetal Muscle Trunk	muscle
24	chr2:191394800-191398600	Weak transcription	Esophagus	oesophagus
25	chr2:191394800-191398600	Weak transcription	Gastric	stomach
26	chr2:191395200-191398200	Weak transcription	NHLF	lung
27	chr2:191395200-191398400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr2:191395200-191398400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr2:191395400-191398200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr2:191395400-191398400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr2:191395400-191398400	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr2:191395400-191398400	Weak transcription	NH-A	brain
33	chr2:191395400-191398600	Weak transcription	HSMMtube	muscle
34	chr2:191395600-191398200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr2:191395600-191398200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr2:191395600-191398200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr2:191395600-191398200	Weak transcription	Muscle Satellite Cultured Cells	--
38	chr2:191395600-191398200	Weak transcription	Brain Hippocampus Middle	brain
39	chr2:191395600-191398200	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr2:191395600-191398200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr2:191395600-191398200	Weak transcription	Placenta Amnion	Placenta Amnion
42	chr2:191395600-191398200	Weak transcription	Monocytes-CD14+_RO01746	blood
43	chr2:191395600-191398400	Weak transcription	Brain Anterior Caudate	brain
44	chr2:191395600-191398400	Weak transcription	Brain Cingulate Gyrus	brain
45	chr2:191395600-191398400	Weak transcription	Lung	lung
46	chr2:191395600-191398400	Weak transcription	Hela-S3	cervix
47	chr2:191395600-191398400	Weak transcription	HSMM	muscle
48	chr2:191395600-191398400	Weak transcription	NHDF-Ad	bronchial
49	chr2:191395600-191398600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr2:191395800-191398200	Weak transcription	Primary monocytes fromperipheralblood	blood

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