Variant report

Variant	rs928596
Chromosome Location	chr1:155947875-155947876
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	POLR2A	chr1:155945649-155950249	K562	blood:	n/a	n/a
2	POLR2A	chr1:155947677-155949686	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr1:155946498-155950066	GM19099	blood:	n/a	n/a
4	SIN3AK20	chr1:155947724-155948406	A549	lung:	n/a	n/a
5	POLR2A	chr1:155947712-155947987	U87	brain:	n/a	n/a
6	ETS1	chr1:155947812-155948477	K562	blood:	n/a	chr1:155948398-155948409 chr1:155948379-155948390 chr1:155948323-155948332 chr1:155948322-155948335
7	POLR2A	chr1:155945717-155950149	K562	blood:	n/a	n/a
8	REST	chr1:155944316-155949059	H1-neurons	neurons:	n/a	chr1:155948423-155948436 chr1:155947302-155947315 chr1:155948473-155948486 chr1:155947032-155947040 chr1:155948493-155948506
9	WRNIP1	chr1:155944973-155947896	GM12878	blood:	n/a	n/a
10	BHLHE40	chr1:155947849-155948645	GM12878	blood:	n/a	chr1:155948537-155948553
11	SMARCB1	chr1:155946884-155949108	Hela-S3	cervix:	n/a	n/a
12	POLR2A	chr1:155947477-155950073	GM18526	blood:	n/a	n/a
13	ZNF143	chr1:155947681-155947907	H1-hESC	embryonic stem cell:	n/a	chr1:155947804-155947814
14	YY1	chr1:155947539-155947879	GM12891	blood:	n/a	chr1:155947682-155947691
15	NFATC1	chr1:155947019-155947881	GM12878	blood:	n/a	n/a
16	TAF1	chr1:155947686-155948540	H1-hESC	embryonic stem cell:	n/a	n/a
17	RUNX3	chr1:155947285-155947907	GM12878	blood:	n/a	n/a
18	TAF1	chr1:155947629-155948859	K562	blood:	n/a	n/a
19	POLR2A	chr1:155947045-155949602	Hela-S3	cervix:	n/a	n/a
20	POLR2A	chr1:155943560-155949842	HL-60	blood:	n/a	n/a
21	POLR2A	chr1:155947551-155947955	H1-hESC	embryonic stem cell:	n/a	n/a
22	POLR2A	chr1:155946479-155949669	GM12891	blood:	n/a	n/a
23	YY1	chr1:155947428-155947883	GM12878	blood:	n/a	chr1:155947682-155947691
24	POLR2A	chr1:155947708-155948629	A549	lung:	n/a	n/a
25	TCF12	chr1:155947644-155948843	ECC-1	luminal epithelium:	n/a	n/a
26	MAZ	chr1:155944495-155949843	IMR90	lung:	n/a	chr1:155944774-155944784 chr1:155945544-155945554
27	YY1	chr1:155947447-155947975	H1-hESC	embryonic stem cell:	n/a	chr1:155947682-155947691
28	POLR2A	chr1:155947712-155949172	HepG2	liver:	n/a	n/a
29	POLR2A	chr1:155947757-155949175	SK-N-SH	brain:	n/a	n/a
30	BCLAF1	chr1:155947524-155948833	GM12878	blood:	n/a	chr1:155948414-155948423
31	TAF1	chr1:155947257-155948829	H1-neurons	neurons:	n/a	n/a
32	TAF1	chr1:155947627-155948687	ECC-1	luminal epithelium:	n/a	n/a
33	STAT5A	chr1:155945377-155950185	GM12878	blood:	n/a	chr1:155946053-155946065 chr1:155946051-155946063 chr1:155949809-155949817 chr1:155949268-155949276 chr1:155946455-155946466 chr1:155948325-155948332 chr1:155947672-155947684 chr1:155946644-155946656 chr1:155945901-155945913 chr1:155947305-155947317
34	POLR2A	chr1:155947411-155948761	H1-hESC	embryonic stem cell:	n/a	n/a
35	POLR2A	chr1:155946637-155949404	H1-hESC	embryonic stem cell:	n/a	n/a
36	POLR2A	chr1:155947252-155950057	GM15510	blood:	n/a	n/a
37	ZBTB7A	chr1:155947309-155949098	ECC-1	luminal epithelium:	n/a	chr1:155947740-155947751
38	RELA	chr1:155947308-155950040	GM12891	blood:	n/a	n/a
39	POLR2A	chr1:155945399-155950018	SK-N-MC	brain:	n/a	n/a
40	POLR2A	chr1:155947553-155949202	K562	blood:	n/a	n/a
41	POLR2A	chr1:155946273-155950193	GM18505	blood:	n/a	n/a
42	POLR2A	chr1:155947642-155948727	HUVEC	blood vessel:	n/a	n/a
43	GABPA	chr1:155947758-155948759	MCF-7	breast:	n/a	chr1:155948065-155948074
44	POLR2A	chr1:155946473-155950087	GM12892	blood:	n/a	n/a
45	POLR2A	chr1:155945870-155950163	GM12878	blood:	n/a	n/a
46	POLR2A	chr1:155947242-155949283	HUVEC	blood vessel:	n/a	n/a
47	MAZ	chr1:155947332-155949741	GM12878	blood:	n/a	n/a
48	POLR2A	chr1:155947542-155948720	Hela-S3	cervix:	n/a	n/a
49	POLR2A	chr1:155947610-155948652	ProgFib	skin:	n/a	n/a
50	TAF1	chr1:155946858-155948472	H1-neurons	neurons:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:155911219..155915431-chr1:155946632..155949866,4	MCF-7	breast:
2	chr1:155946065..155948960-chr1:156022753..156025097,3	MCF-7	breast:
3	chr1:155902613..155905963-chr1:155944776..155950602,8	MCF-7	breast:
4	chr1:155902096..155906333-chr1:155944635..155950706,8	K562	blood:
5	chr1:155902752..155906488-chr1:155946119..155948945,5	MCF-7	breast:
6	chr1:155945057..155948418-chr1:156022747..156026553,6	K562	blood:
7	chr1:155946982..155950141-chr1:156022442..156025223,4	MCF-7	breast:
8	chr1:155946078..155947877-chr1:155959133..155960966,2	MCF-7	breast:
9	chr1:155907837..155914260-chr1:155947632..155952579,11	MCF-7	breast:
10	chr1:155946653..155948454-chr1:155959056..155961851,2	K562	blood:
11	chr1:155947571..155948767-chr11:62608644..62609651,3	Hela-S3	cervix:
12	chr1:155902760..155905677-chr1:155945999..155951456,7	K562	blood:
13	chr1:155945057..155948418-chr1:156022741..156026553,6	K562	blood:
14	chr1:155879661..155882760-chr1:155946571..155949454,3	K562	blood:
15	chr1:155947439..155949635-chr1:156095639..156097147,2	MCF-7	breast:
16	chr1:155947462..155948981-chr1:155988389..155991184,2	K562	blood:
17	chr1:155947454..155949209-chr1:155971698..155973677,2	K562	blood:

Variant related genes	Relation type
ENSG00000273002	TF binding region
ENSG00000116586	Chromatin interaction
ENSG00000132680	Chromatin interaction
ENSG00000163479	Chromatin interaction
ENSG00000224276	Chromatin interaction
ENSG00000160789	Chromatin interaction
ENSG00000160803	Chromatin interaction
ENSG00000173080	Chromatin interaction
ENSG00000116584	Chromatin interaction
ENSG00000143622	Chromatin interaction
ENSG00000133316	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10796955	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1111102	0.86[CEU][hapmap];0.82[TSI][hapmap]
rs11264422	0.93[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs11264426	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.88[TSI][hapmap];0.86[YRI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11585845	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12037177	0.95[CEU][hapmap];0.86[MEX][hapmap];0.85[TSI][hapmap]
rs12118795	0.90[CEU][hapmap];0.85[CHD][hapmap];0.85[TSI][hapmap]
rs12568523	0.95[CEU][hapmap]
rs1749405	0.80[CHB][hapmap]
rs1889532	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1889533	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2016251	0.95[CEU][hapmap];0.86[MEX][hapmap];0.88[TSI][hapmap]
rs2282301	0.95[CEU][hapmap];0.91[MEX][hapmap];0.85[TSI][hapmap]
rs2297649	0.95[CEU][hapmap];0.89[GIH][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2364403	0.82[MEX][hapmap]
rs2993207	0.80[CHB][hapmap]
rs3856261	0.88[JPT][hapmap]
rs4661175	0.86[ASW][hapmap];0.93[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs4661217	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4661218	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs488079	0.80[CHB][hapmap]
rs490498	0.93[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap]
rs539602	0.80[CHB][hapmap]
rs61813286	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs625658	0.80[CHB][hapmap]
rs6427297	0.81[CEU][hapmap]
rs6667652	0.95[CEU][hapmap];0.91[MEX][hapmap];0.85[TSI][hapmap]
rs6670493	1.00[CEU][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6696019	0.95[CEU][hapmap]
rs670523	0.93[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap]
rs729022	0.82[MEX][hapmap]
rs7534858	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs822478	0.89[JPT][hapmap]
rs867549	0.95[CEU][hapmap];0.91[MEX][hapmap]
rs867550	0.95[CEU][hapmap];0.91[MEX][hapmap]
rs915178	0.86[CEU][hapmap]
rs915181	0.95[CEU][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916198	chr1:155804210-156403997	Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	428 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs928596	RIT1	Cis_1M	lymphoblastoid	RTeQTL
rs928596	YY1AP1	cis	cerebellum	SCAN
rs928596	PRUNE	cis	cerebellum	SCAN
rs928596	ROBLD3	cis	parietal	SCAN
rs928596	SPRR3	cis	parietal	SCAN
rs928596	RIT1	cis	cerebellum	SCAN
rs928596	RIT1	cis	Thyroid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:155943600-155951400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr1:155944000-155949200	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
3	chr1:155944600-155949400	Active TSS	Aorta	Aorta
4	chr1:155944800-155950000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
5	chr1:155945200-155948600	Active TSS	Fetal Brain Female	brain
6	chr1:155945200-155948800	Active TSS	Fetal Kidney	kidney
7	chr1:155945200-155950800	Flanking Active TSS	Stomach Smooth Muscle	stomach
8	chr1:155945400-155948600	Active TSS	Thymus	Thymus
9	chr1:155945600-155948600	Active TSS	Brain Angular Gyrus	brain
10	chr1:155945600-155949000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr1:155945600-155949000	Active TSS	Primary T killer naive cells fromperipheralblood	blood
12	chr1:155945600-155949000	Active TSS	Pancreatic Islets	Pancreatic Islet
13	chr1:155945600-155949000	Active TSS	HSMMtube	muscle
14	chr1:155945600-155949200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr1:155945600-155949200	Active TSS	H9 Cell Line	embryonic stem cell
16	chr1:155945600-155949200	Active TSS	Primary T helper naive cells from peripheral blood	blood
17	chr1:155945800-155948600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr1:155945800-155948800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr1:155945800-155948800	Active TSS	Ovary	ovary
20	chr1:155945800-155949200	Active TSS	ES-I3 Cell Line	embryonic stem cell
21	chr1:155945800-155949200	Active TSS	Primary T helper cells PMA-I stimulated	--
22	chr1:155945800-155949200	Active TSS	Small Intestine	intestine
23	chr1:155946000-155948600	Active TSS	Primary monocytes fromperipheralblood	blood
24	chr1:155946000-155948800	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
25	chr1:155946000-155948800	Transcr. at gene 5' and 3'	Primary T helper naive cells fromperipheralblood	blood
26	chr1:155946000-155948800	Active TSS	Brain Substantia Nigra	brain
27	chr1:155946000-155948800	Active TSS	Lung	lung
28	chr1:155946000-155949000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr1:155946000-155949000	Active TSS	Primary T killer memory cells from peripheral blood	blood
30	chr1:155946000-155949000	Active TSS	Gastric	stomach
31	chr1:155946000-155949600	Active TSS	GM12878-XiMat	blood
32	chr1:155946200-155948400	Transcr. at gene 5' and 3'	Primary T regulatory cells fromperipheralblood	blood
33	chr1:155946200-155948600	Active TSS	Primary T cells from cord blood	blood
34	chr1:155946200-155948800	Active TSS	Primary B cells from peripheral blood	blood
35	chr1:155946200-155949000	Active TSS	NHDF-Ad	bronchial
36	chr1:155946400-155949400	Active TSS	Right Atrium	heart
37	chr1:155946600-155948000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
38	chr1:155947000-155948800	Active TSS	HUES64 Cell Line	embryonic stem cell
39	chr1:155947000-155949000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr1:155947000-155949000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr1:155947200-155948000	Active TSS	Fetal Brain Male	brain
42	chr1:155947200-155948400	Active TSS	Primary T cells fromperipheralblood	blood
43	chr1:155947200-155948400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr1:155947200-155948400	Active TSS	Fetal Thymus	thymus
45	chr1:155947200-155948600	Active TSS	Primary neutrophils fromperipheralblood	blood
46	chr1:155947200-155948600	Active TSS	Muscle Satellite Cultured Cells	--
47	chr1:155947200-155948600	Active TSS	Brain Hippocampus Middle	brain
48	chr1:155947200-155948600	Active TSS	Fetal Muscle Trunk	muscle
49	chr1:155947200-155948600	Active TSS	Monocytes-CD14+_RO01746	blood
50	chr1:155947200-155948800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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