Variant report

Variant	rs9845862
Chromosome Location	chr3:136472573-136472574
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SMC3	chr3:136469791-136472601	Hela-S3	cervix:	n/a	chr3:136471189-136471203 chr3:136470573-136470583 chr3:136471247-136471261 chr3:136471196-136471203
2	TAL1	chr3:136469847-136472703	K562	blood:	n/a	chr3:136471188-136471203 chr3:136471188-136471203 chr3:136471188-136471203
3	POLR2A	chr3:136468906-136472752	PBDE	blood:	n/a	n/a
4	RAD21	chr3:136471015-136472693	Hela-S3	cervix:	n/a	chr3:136471510-136471523 chr3:136471185-136471204 chr3:136471188-136471201 chr3:136471511-136471525 chr3:136471245-136471257 chr3:136471189-136471203 chr3:136471513-136471527 chr3:136471247-136471261 chr3:136471243-136471262
5	POLR2A	chr3:136470008-136472743	K562	blood:	n/a	n/a
6	POLR2A	chr3:136469861-136473110	HepG2	liver:	n/a	n/a
7	SMC3	chr3:136470971-136472600	GM12878	blood:	n/a	chr3:136471189-136471203 chr3:136471247-136471261 chr3:136471196-136471203
8	TBP	chr3:136470033-136473040	K562	blood:	n/a	n/a
9	POLR2A	chr3:136468959-136472839	GM12891	blood:	n/a	n/a
10	POLR2A	chr3:136469846-136473025	H1-hESC	embryonic stem cell:	n/a	n/a
11	POLR2A	chr3:136470032-136472652	GM19099	blood:	n/a	n/a
12	POLR2A	chr3:136469618-136472614	IMR90	lung:	n/a	n/a
13	SMC3	chr3:136469659-136472745	SK-N-SH	brain:	n/a	chr3:136471189-136471203 chr3:136470573-136470583 chr3:136471247-136471261 chr3:136471196-136471203
14	POLR2A	chr3:136469829-136473142	SK-N-MC	brain:	n/a	n/a
15	RCOR1	chr3:136470074-136472682	K562	blood:	n/a	n/a
16	POLR2A	chr3:136469945-136472998	PANC-1	pancreas:	n/a	n/a
17	POLR2A	chr3:136469974-136472864	GM12878	blood:	n/a	n/a
18	POLR2A	chr3:136471117-136472963	K562	blood:	n/a	n/a
19	POLR2A	chr3:136469922-136472817	GM12878	blood:	n/a	n/a
20	POLR2A	chr3:136470004-136472911	K562	blood:	n/a	n/a
21	POLR2A	chr3:136472524-136472670	HUVEC	blood vessel:	n/a	n/a
22	POLR2A	chr3:136470043-136472953	K562	blood:	n/a	n/a
23	POLR2A	chr3:136469618-136472918	PANC-1	pancreas:	n/a	n/a
24	POLR2A	chr3:136469959-136472592	HUVEC	blood vessel:	n/a	n/a
25	MYC	chr3:136469203-136472639	K562	blood:	n/a	chr3:136470730-136470740 chr3:136470527-136470536 chr3:136470260-136470270 chr3:136471424-136471434
26	MAX	chr3:136469821-136472637	NB4	blood:	n/a	chr3:136470730-136470740 chr3:136470527-136470536 chr3:136470260-136470270 chr3:136471424-136471434
27	MYC	chr3:136469902-136472744	NB4	blood:	n/a	chr3:136470730-136470740 chr3:136470527-136470536 chr3:136470260-136470270 chr3:136471424-136471434
28	IRF1	chr3:136472335-136472814	K562	blood:	n/a	n/a
29	HEY1	chr3:136470019-136472905	K562	blood:	n/a	chr3:136471680-136471695 chr3:136471334-136471349 chr3:136471149-136471164 chr3:136471382-136471397
30	RUNX3	chr3:136470791-136472632	GM12878	blood:	n/a	n/a
31	RELA	chr3:136470065-136472578	GM12891	blood:	n/a	chr3:136470402-136470411 chr3:136470402-136470411
32	POLR2A	chr3:136470678-136472718	GM12892	blood:	n/a	n/a
33	GATA2	chr3:136471094-136472745	SH-SY5Y	brain:	n/a	n/a
34	MYC	chr3:136472422-136472981	K562	blood:	n/a	n/a
35	POLR2A	chr3:136472564-136473016	ECC-1	luminal epithelium:	n/a	n/a
36	WRNIP1	chr3:136471147-136472762	GM12878	blood:	n/a	n/a
37	POLR2A	chr3:136470007-136472973	GM12892	blood:	n/a	n/a
38	MXI1	chr3:136469517-136472913	SK-N-SH	brain:	n/a	chr3:136472194-136472203
39	POLR2A	chr3:136469758-136472840	K562	blood:	n/a	n/a
40	GATA1	chr3:136471100-136472849	PBDE	blood:	n/a	n/a
41	POLR2A	chr3:136470782-136472736	PFSK-1	brain:	n/a	n/a
42	POLR2A	chr3:136469984-136472741	GM12878	blood:	n/a	n/a
43	POLR2A	chr3:136470081-136472945	MCF-7	breast:	n/a	n/a
44	POLR2A	chr3:136468958-136472707	MCF10A-Er-Src	breast:	n/a	n/a
45	POLR2A	chr3:136470657-136472624	GM12878	blood:	n/a	n/a
46	CHD1	chr3:136468843-136472737	IMR90	lung:	n/a	chr3:136470257-136470267
47	POLR2A	chr3:136469802-136472619	Hela-S3	cervix:	n/a	n/a
48	POLR2A	chr3:136469856-136472661	Hela-S3	cervix:	n/a	n/a
49	POLR2A	chr3:136470170-136472592	GM12878	blood:	n/a	n/a
50	POLR2A	chr3:136470003-136473184	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:136466613..136474326-chr3:136579481..136583133,10	K562	blood:
2	chr3:136472151..136474742-chr3:136749777..136751390,2	K562	blood:
3	chr3:136471389..136473293-chr3:136580852..136582413,2	MCF-7	breast:
4	chr3:136468701..136475672-chr3:136535815..136540749,9	K562	blood:
5	chr3:136350170..136353597-chr3:136468835..136472616,3	MCF-7	breast:
6	chr3:135912902..135916874-chr3:136469598..136473232,8	MCF-7	breast:
7	chr3:136469311..136474326-chr3:136579207..136583133,7	K562	blood:
8	chr3:135912817..135916962-chr3:136469681..136473212,8	K562	blood:
9	chr3:136277326..136280102-chr3:136471685..136473348,2	MCF-7	breast:
10	chr3:135969104..135971090-chr3:136470031..136473091,3	MCF-7	breast:
11	chr3:136469358..136473351-chr3:136579831..136582888,9	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TMEM22-1	chr3:136471472-136474622	ENSG00000261758.1
2	lnc-TMEM22-1	chr3:136472487-136472720	NONHSAT092283

Variant related genes	Relation type
STAG1	TF binding region
ENSG00000251708	Chromatin interaction
ENSG00000158092	Chromatin interaction
ENSG00000168917	Chromatin interaction
ENSG00000239213	Chromatin interaction
ENSG00000114054	Chromatin interaction
ENSG00000174579	Chromatin interaction

Extended variants
information (count: 84 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs1052620	0.93[CEU][hapmap];0.96[GIH][hapmap];0.91[MEX][hapmap];1.00[ASN][1000 genomes]
rs12695649	1.00[ASN][1000 genomes]
rs13062352	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13066401	1.00[ASN][1000 genomes]
rs13071220	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.89[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs13080786	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13092193	1.00[ASN][1000 genomes]
rs13096466	1.00[ASN][1000 genomes]
rs13100192	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13314357	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13326151	1.00[ASN][1000 genomes]
rs13433683	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13433688	1.00[CEU][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13434116	1.00[ASN][1000 genomes]
rs17365792	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1872239	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2176269	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28370972	1.00[ASN][1000 genomes]
rs28390205	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28472992	1.00[ASN][1000 genomes]
rs28489326	1.00[ASN][1000 genomes]
rs28641809	1.00[ASN][1000 genomes]
rs28750366	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[GIH][hapmap];0.81[LWK][hapmap];0.91[MEX][hapmap];0.90[MKK][hapmap];0.87[TSI][hapmap];1.00[ASN][1000 genomes]
rs28811905	1.00[ASN][1000 genomes]
rs28877020	1.00[ASN][1000 genomes]
rs34564818	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34645606	1.00[ASN][1000 genomes]
rs34804893	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[GIH][hapmap];0.91[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34969907	1.00[ASN][1000 genomes]
rs35096613	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35100027	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35198484	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35210994	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35422852	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35428413	0.90[AFR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35880395	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36109616	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36177165	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4038586	0.84[ASW][hapmap];0.93[CEU][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.89[MKK][hapmap];0.87[TSI][hapmap];1.00[ASN][1000 genomes]
rs4470449	1.00[ASN][1000 genomes]
rs66509730	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67145204	1.00[ASN][1000 genomes]
rs67382287	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6767889	1.00[ASN][1000 genomes]
rs6771002	1.00[ASN][1000 genomes]
rs6773949	1.00[ASN][1000 genomes]
rs6774964	1.00[ASN][1000 genomes]
rs6806123	0.93[CEU][hapmap];0.82[GIH][hapmap];0.91[MEX][hapmap];1.00[ASN][1000 genomes]
rs71310215	0.81[AMR][1000 genomes]
rs71336069	1.00[ASN][1000 genomes]
rs71336080	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73230043	1.00[ASN][1000 genomes]
rs73230099	1.00[ASN][1000 genomes]
rs73231903	1.00[ASN][1000 genomes]
rs7612425	1.00[ASN][1000 genomes]
rs9289513	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9809269	1.00[ASN][1000 genomes]
rs9809988	0.93[CEU][hapmap];0.85[YRI][hapmap];0.81[AFR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9813376	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9813691	1.00[ASN][1000 genomes]
rs9819856	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9820717	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.81[LWK][hapmap];0.91[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9828088	1.00[ASN][1000 genomes]
rs9828976	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9838884	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9840500	1.00[ASN][1000 genomes]
rs9847427	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9850364	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9857833	0.90[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs9857966	0.93[CEU][hapmap];0.82[GIH][hapmap];0.91[MEX][hapmap];1.00[ASN][1000 genomes]
rs9858560	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9860879	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9865995	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9867325	0.93[CEU][hapmap];1.00[ASN][1000 genomes]
rs9869630	1.00[ASN][1000 genomes]
rs9871184	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9873536	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9875770	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9878078	1.00[ASN][1000 genomes]
rs9879531	1.00[ASN][1000 genomes]
rs9881831	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9883189	0.93[CEU][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];1.00[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	nsv877529	chr3:136364511-136487559	ZNF genes & repeats Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
2	nsv1006737	chr3:136466188-136530743	Active TSS Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9845862	ERICH1	trans	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:136468200-136473000	Active TSS	A549	lung
2	chr3:136468400-136472600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr3:136469000-136472600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr3:136469000-136472600	Active TSS	Colonic Mucosa	Colon
5	chr3:136469200-136473000	Active TSS	H9 Cell Line	embryonic stem cell
6	chr3:136469200-136473400	Active TSS	K562	blood
7	chr3:136469400-136472600	Active TSS	ES-I3 Cell Line	embryonic stem cell
8	chr3:136469400-136472600	Active TSS	HSMMtube	muscle
9	chr3:136470000-136472600	Active TSS	Pancreas	Pancrea
10	chr3:136470000-136472800	Active TSS	Pancreatic Islets	Pancreatic Islet
11	chr3:136471600-136473000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr3:136471800-136472600	Flanking Active TSS	Primary T cells from cord blood	blood
13	chr3:136471800-136472600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
14	chr3:136471800-136472600	Flanking Active TSS	Fetal Brain Male	brain
15	chr3:136471800-136472600	Flanking Active TSS	Placenta	Placenta
16	chr3:136471800-136472600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
17	chr3:136471800-136472800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr3:136471800-136472800	Flanking Active TSS	Rectal Smooth Muscle	rectum
19	chr3:136471800-136472800	Flanking Active TSS	HUVEC	blood vessel
20	chr3:136471800-136472800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
21	chr3:136471800-136472800	Flanking Active TSS	NH-A	brain
22	chr3:136471800-136473000	Flanking Active TSS	Duodenum Mucosa	Duodenum
23	chr3:136471800-136473000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
24	chr3:136472000-136472600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr3:136472000-136472600	Flanking Active TSS	Primary hematopoietic stem cells	blood
26	chr3:136472000-136472600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
27	chr3:136472000-136472600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
28	chr3:136472000-136472600	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
29	chr3:136472000-136472600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
30	chr3:136472000-136472600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr3:136472000-136472600	Flanking Active TSS	Brain Hippocampus Middle	brain
32	chr3:136472000-136472600	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
33	chr3:136472000-136472600	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
34	chr3:136472000-136472600	Flanking Active TSS	Fetal Heart	heart
35	chr3:136472000-136472600	Flanking Active TSS	Fetal Intestine Small	intestine
36	chr3:136472000-136472600	Flanking Active TSS	Fetal Lung	lung
37	chr3:136472000-136472600	Flanking Active TSS	Fetal Muscle Leg	muscle
38	chr3:136472000-136472600	Flanking Active TSS	Fetal Thymus	thymus
39	chr3:136472000-136472600	Flanking Active TSS	Placenta Amnion	Placenta Amnion
40	chr3:136472000-136472600	Weak transcription	Spleen	Spleen
41	chr3:136472000-136472600	Flanking Active TSS	HMEC	breast
42	chr3:136472000-136472600	Flanking Active TSS	NHDF-Ad	bronchial
43	chr3:136472000-136472600	Flanking Active TSS	NHLF	lung
44	chr3:136472000-136472600	Flanking Active TSS	Osteobl	bone
45	chr3:136472000-136472800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr3:136472000-136472800	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
47	chr3:136472000-136472800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
48	chr3:136472000-136472800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr3:136472000-136472800	Flanking Active TSS	Fetal Kidney	kidney
50	chr3:136472000-136472800	Weak transcription	Lung	lung

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