Variant report

Variant	rs360129
Chromosome Location	chr11:9809956-9809957
allele	A/G
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	GATA3	chr11:9809229-9810180	SK-N-SH	brain:	n/a	chr11:9809593-9809600
2	REST	chr11:9809256-9810103	PFSK-1	brain:	n/a	chr11:9809374-9809392
3	POLR2A	chr11:9809758-9810195	HL-60	blood:	n/a	n/a
4	EP300	chr11:9809450-9810124	SK-N-SH_RA	brain:	n/a	n/a
5	REST	chr11:9809725-9810046	SK-N-SH	brain:	n/a	n/a
6	RCOR1	chr11:9809217-9810219	IMR90	lung:	n/a	n/a
7	TEAD4	chr11:9809365-9810249	SK-N-SH	brain:	n/a	n/a
8	MAX	chr11:9809295-9810121	SK-N-SH	brain:	n/a	chr11:9809738-9809747
9	PBX3	chr11:9809291-9810174	SK-N-SH	brain:	n/a	n/a
10	TEAD4	chr11:9809289-9810241	SK-N-SH	brain:	n/a	n/a
11	MEF2A	chr11:9809427-9810191	SK-N-SH	brain:	n/a	n/a
12	RXRA	chr11:9809313-9810163	SK-N-SH	brain:	n/a	chr11:9809606-9809622
13	RAD21	chr11:9809496-9809963	SK-N-SH_RA	brain:	n/a	n/a
14	POLR2A	chr11:9809558-9810229	U87	brain:	n/a	n/a
15	NFIC	chr11:9809260-9810245	SK-N-SH	brain:	n/a	n/a
16	EP300	chr11:9809249-9810226	SK-N-SH	brain:	n/a	n/a
17	RXRA	chr11:9809273-9810193	SK-N-SH	brain:	n/a	chr11:9809606-9809622
18	REST	chr11:9809484-9810014	SK-N-SH	brain:	n/a	n/a
19	USF1	chr11:9809592-9810012	SK-N-SH	brain:	n/a	n/a
20	FOSL2	chr11:9809456-9810144	SK-N-SH	brain:	n/a	n/a
21	POLR2A	chr11:9809722-9810145	U87	brain:	n/a	n/a
22	EP300	chr11:9809407-9810143	SK-N-SH_RA	brain:	n/a	n/a
23	GATA3	chr11:9808762-9810226	SK-N-SH	brain:	n/a	chr11:9809593-9809600
24	EP300	chr11:9809275-9810180	SK-N-SH	brain:	n/a	n/a
25	SIN3AK20	chr11:9809449-9810044	SK-N-SH	brain:	n/a	n/a
26	JUND	chr11:9809367-9810220	SK-N-SH	brain:	n/a	n/a
27	NFIC	chr11:9809286-9810137	SK-N-SH	brain:	n/a	n/a
28	TCF12	chr11:9808762-9810365	SK-N-SH	brain:	n/a	chr11:9809764-9809774 chr11:9809780-9809790 chr11:9809436-9809444
29	POLR2A	chr11:9809723-9810170	HL-60	blood:	n/a	n/a
30	FOSL2	chr11:9809378-9810141	SK-N-SH	brain:	n/a	n/a
31	POLR2A	chr11:9809370-9810164	SK-N-SH	brain:	n/a	n/a
32	POLR2A	chr11:9809681-9810110	U87	brain:	n/a	n/a
33	POLR2A	chr11:9809406-9809976	PFSK-1	brain:	n/a	n/a
34	TCF12	chr11:9809196-9810260	SK-N-SH	brain:	n/a	chr11:9809764-9809774 chr11:9809780-9809790 chr11:9809436-9809444
35	MAX	chr11:9809421-9810163	SK-N-SH	brain:	n/a	chr11:9809738-9809747
36	RAD21	chr11:9809847-9810042	IMR90	lung:	n/a	n/a
37	POLR2A	chr11:9809461-9810085	SK-N-SH	brain:	n/a	n/a
38	PBX3	chr11:9809320-9810185	SK-N-SH	brain:	n/a	n/a
39	CTCF	chr11:9809840-9809990	AG09319	gingival:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:9807438..9810264-chr11:10314419..10316538,2	MCF-7	breast:

Variant related genes	Relation type
SBF2	TF binding region
ENSG00000133812	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10118	0.84[CHB][hapmap];0.90[CHD][hapmap];0.89[JPT][hapmap];0.92[ASN][1000 genomes]
rs10770062	0.89[CEU][hapmap];0.94[CHB][hapmap];0.87[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.94[ASN][1000 genomes]
rs1392026	0.93[ASN][1000 genomes]
rs183110	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1875030	0.91[ASN][1000 genomes]
rs2173030	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2645017	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2645029	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs360120	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs360124	0.86[ASW][hapmap];1.00[CHB][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs360127	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs360130	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs360131	0.99[ASN][1000 genomes]
rs360132	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs360140	0.95[CHB][hapmap];0.85[JPT][hapmap]
rs360141	0.92[ASN][1000 genomes]
rs360142	0.86[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs360143	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs360146	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs360150	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs360151	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs360158	0.95[CHB][hapmap]
rs380806	0.90[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs391304	0.80[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs394315	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs432849	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs438151	0.90[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs446760	1.00[CEU][hapmap];0.90[CHB][hapmap];0.92[EUR][1000 genomes]
rs472487	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs634680	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6483726	0.85[CHB][hapmap];0.88[CHD][hapmap];0.90[JPT][hapmap];0.85[MEX][hapmap];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933855	chr11:9645441-10130519	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv1053369	chr11:9647837-9876054	Genic enhancers Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv553468	chr11:9667828-9827871	Weak transcription Genic enhancers Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
4	nsv896987	chr11:9759918-9885849	Strong transcription Enhancers Genic enhancers Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
5	esv3384280	chr11:9766350-9911228	Flanking Bivalent TSS/Enh Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs360129	PPFIBP2	cis	cerebellum	SCAN
rs360129	CNGA4	cis	parietal	SCAN
rs360129	C11orf17	cis	parietal	SCAN
rs360129	CSNK2A1P	cis	parietal	SCAN
rs360129	MRPL17	cis	cerebellum	SCAN

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:9780600-9813200	Weak transcription	Small Intestine	intestine
2	chr11:9795200-9812800	Strong transcription	Monocytes-CD14+_RO01746	blood
3	chr11:9797400-9821800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
4	chr11:9797800-9811800	Strong transcription	Cortex derived primary cultured neurospheres	brain
5	chr11:9798200-9810400	Strong transcription	Primary monocytes fromperipheralblood	blood
6	chr11:9798600-9811600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr11:9799200-9812000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr11:9799200-9812200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr11:9799600-9810600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr11:9799600-9823400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr11:9799800-9811600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr11:9799800-9812000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr11:9799800-9812200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chr11:9799800-9812200	Strong transcription	Liver	Liver
15	chr11:9799800-9814200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr11:9800200-9823800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr11:9801600-9823800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
18	chr11:9802600-9810600	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr11:9802800-9810200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr11:9803000-9823400	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr11:9803000-9823400	Weak transcription	Psoas Muscle	Psoas
22	chr11:9803200-9811400	Weak transcription	Brain Substantia Nigra	brain
23	chr11:9803200-9828600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr11:9803200-9828600	Weak transcription	Gastric	stomach
25	chr11:9803200-9828800	Weak transcription	Primary T cells fromperipheralblood	blood
26	chr11:9803400-9811200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr11:9804600-9812000	Strong transcription	Fetal Lung	lung
28	chr11:9804800-9810200	Strong transcription	Primary T cells from cord blood	blood
29	chr11:9804800-9811800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr11:9804800-9811800	Strong transcription	Fetal Intestine Small	intestine
31	chr11:9804800-9811800	Strong transcription	Rectal Mucosa Donor 29	rectum
32	chr11:9804800-9812000	Strong transcription	Primary neutrophils fromperipheralblood	blood
33	chr11:9805000-9811000	Strong transcription	Brain Cingulate Gyrus	brain
34	chr11:9805000-9811600	Strong transcription	H9 Cell Line	embryonic stem cell
35	chr11:9805000-9811600	Strong transcription	Fetal Brain Female	brain
36	chr11:9805000-9811800	Strong transcription	Thymus	Thymus
37	chr11:9805000-9812200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
38	chr11:9805000-9812800	Strong transcription	HepG2	liver
39	chr11:9805000-9815600	Strong transcription	Fetal Intestine Large	intestine
40	chr11:9805200-9811800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr11:9805200-9815600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr11:9806200-9810800	Strong transcription	Duodenum Mucosa	Duodenum
43	chr11:9806800-9821400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr11:9806800-9828600	Weak transcription	Primary T helper cells PMA-I stimulated	--
45	chr11:9807200-9823200	Weak transcription	Fetal Heart	heart
46	chr11:9807800-9810600	Weak transcription	Primary B cells from cord blood	blood
47	chr11:9807800-9811800	Strong transcription	HUES6 Cell Line	embryonic stem cell
48	chr11:9807800-9811800	Strong transcription	Ovary	ovary
49	chr11:9807800-9811800	Strong transcription	NHEK	skin
50	chr11:9808000-9810800	Strong transcription	H1 Cell Line	embryonic stem cell

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