Variant report

Variant	rs10929699
Chromosome Location	chr2:10918209-10918210
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	chr2:10918168-10918288	Hela-S3	cervix:	n/a	n/a
2	CCNT2	chr2:10918145-10918443	K562	blood:	n/a	n/a
3	POLR2A	chr2:10918091-10918564	A549	lung:	n/a	n/a
4	POLR2A	chr2:10918138-10918334	HCT-116	colon:	n/a	n/a
5	POLR2A	chr2:10918125-10919017	GM18505	blood:	n/a	n/a
6	POLR2A	chr2:10917705-10918509	GM12878	blood:	n/a	n/a
7	POLR2A	chr2:10916307-10919284	K562	blood:	n/a	n/a
8	POLR2A	chr2:10918153-10918448	HepG2	liver:	n/a	n/a
9	POLR2A	chr2:10917972-10919234	HL-60	blood:	n/a	n/a
10	POLR2A	chr2:10915153-10919303	K562	blood:	n/a	n/a
11	POLR2A	chr2:10918209-10918239	MCF-7	breast:	n/a	n/a
12	POLR2A	chr2:10918189-10918698	GM12892	blood:	n/a	n/a
13	POLR2A	chr2:10918192-10918466	GM12892	blood:	n/a	n/a
14	POLR2A	chr2:10918111-10918768	K562	blood:	n/a	n/a
15	POLR2A	chr2:10918076-10918474	HepG2	liver:	n/a	n/a
16	POLR2A	chr2:10918179-10918515	GM12878	blood:	n/a	n/a
17	POLR2A	chr2:10916350-10919110	SK-N-MC	brain:	n/a	n/a
18	POLR2A	chr2:10918160-10918441	HepG2	liver:	n/a	n/a
19	POLR2A	chr2:10918012-10919163	GM12892	blood:	n/a	n/a
20	POLR2A	chr2:10918013-10918560	GM12878	blood:	n/a	n/a
21	POLR2A	chr2:10918091-10918283	HUVEC	blood vessel:	n/a	n/a
22	POLR2A	chr2:10918054-10918534	GM12878	blood:	n/a	n/a
23	POLR2A	chr2:10918120-10919129	PFSK-1	brain:	n/a	n/a

Variant related genes	Relation type
ATP6V1C2	TF binding region

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs1686484	0.81[CHB][hapmap]
rs1686510	0.95[CHB][hapmap];0.86[ASN][1000 genomes]
rs1686511	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1734340	0.95[CHB][hapmap];0.86[ASN][1000 genomes]
rs1734344	0.95[CEU][hapmap];1.00[CHB][hapmap];0.90[GIH][hapmap];0.84[JPT][hapmap]
rs1734426	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1734427	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1734433	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1734435	0.95[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1734436	0.95[CEU][hapmap];1.00[CHB][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1734439	0.81[CHB][hapmap]
rs1734440	0.91[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1844386	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28652982	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2969881	0.93[ASN][1000 genomes]
rs2969882	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4668695	0.93[ASN][1000 genomes]
rs4807	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6750383	0.94[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	nsv1000953	chr2:10717304-10921805	Strong transcription Enhancers Active TSS Bivalent Enhancer Genic enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	nsv535584	chr2:10717304-10921805	Bivalent Enhancer Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	nsv1000731	chr2:10758657-10943882	Strong transcription Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10929699	RP11-791G15.2	cis	lung	GTEx

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:10906200-10918400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr2:10908000-10918400	Weak transcription	Aorta	Aorta
3	chr2:10908600-10924400	Weak transcription	Psoas Muscle	Psoas
4	chr2:10913200-10920200	Weak transcription	NH-A	brain
5	chr2:10913400-10920200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr2:10913600-10918400	Weak transcription	HSMM	muscle
7	chr2:10913600-10919800	Weak transcription	Osteobl	bone
8	chr2:10914200-10920000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr2:10914600-10918400	Weak transcription	HepG2	liver
10	chr2:10914600-10920200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr2:10914600-10922400	Weak transcription	Fetal Kidney	kidney
12	chr2:10914600-10931600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr2:10914800-10918600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr2:10915000-10920000	Weak transcription	Primary hematopoietic stem cells	blood
15	chr2:10915000-10920000	Weak transcription	Brain Angular Gyrus	brain
16	chr2:10915000-10921600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr2:10915200-10920200	Weak transcription	HSMMtube	muscle
18	chr2:10915200-10923000	Weak transcription	Fetal Brain Male	brain
19	chr2:10915600-10918400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr2:10915600-10918600	Weak transcription	HUES6 Cell Line	embryonic stem cell
21	chr2:10915600-10920000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr2:10915600-10920200	Weak transcription	HMEC	breast
23	chr2:10915600-10920400	Weak transcription	Stomach Mucosa	stomach
24	chr2:10915600-10921800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr2:10915600-10939800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr2:10915600-10950400	Weak transcription	Right Atrium	heart
27	chr2:10915800-10918600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr2:10915800-10920000	Weak transcription	Fetal Lung	lung
29	chr2:10915800-10929000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr2:10916000-10918600	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr2:10916000-10920400	Weak transcription	Hela-S3	cervix
32	chr2:10916000-10921800	Weak transcription	Small Intestine	intestine
33	chr2:10916200-10920000	Weak transcription	HUVEC	blood vessel
34	chr2:10916200-10920400	Weak transcription	Colon Smooth Muscle	Colon
35	chr2:10916200-10939200	Strong transcription	Fetal Stomach	stomach
36	chr2:10916400-10918600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
37	chr2:10916400-10921400	Strong transcription	Fetal Brain Female	brain
38	chr2:10916400-10922200	Weak transcription	Fetal Heart	heart
39	chr2:10916400-10923200	Weak transcription	NHDF-Ad	bronchial
40	chr2:10916400-10923600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr2:10916400-10923600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr2:10916400-10928600	Strong transcription	Fetal Intestine Small	intestine
43	chr2:10916400-10931200	Strong transcription	Cortex derived primary cultured neurospheres	brain
44	chr2:10916400-10931600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr2:10916400-10938600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr2:10916600-10918400	Weak transcription	Primary T cells fromperipheralblood	blood
47	chr2:10916600-10918400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
48	chr2:10916600-10919800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
49	chr2:10916600-10943800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
50	chr2:10916800-10920000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

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