Variant report

Variant	rs1009977
Chromosome Location	chr14:55603002-55603003
allele	G/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	JUND	chr14:55602759-55603574	SK-N-SH	brain:	n/a	chr14:55603144-55603156 chr14:55603146-55603154
2	POLR2A	chr14:55602996-55603048	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr14:55602371-55603020	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr14:55602694-55603197	A549	lung:	n/a	n/a
5	TCF12	chr14:55602778-55603430	SK-N-SH	brain:	n/a	chr14:55602781-55602791
6	POLR2A	chr14:55602951-55603299	SK-N-SH	brain:	n/a	n/a
7	TCF12	chr14:55602798-55603491	SK-N-SH	brain:	n/a	n/a
8	FOSL2	chr14:55602881-55603373	SK-N-SH	brain:	n/a	chr14:55603144-55603156 chr14:55603146-55603154

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:55517047..55520032-chr14:55601675..55604188,2	MCF-7	breast:

Variant related genes	Relation type
LGALS3	TF binding region
ENSG00000168175	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs1009978	0.96[CEU][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10134800	0.90[EUR][1000 genomes]
rs10137409	0.97[EUR][1000 genomes]
rs10140801	0.85[CEU][hapmap];0.95[TSI][hapmap]
rs10140857	0.96[CEU][hapmap];0.82[CHB][hapmap];0.87[EUR][1000 genomes]
rs10140869	0.88[CEU][hapmap]
rs10147667	0.96[CEU][hapmap];0.84[TSI][hapmap];0.89[EUR][1000 genomes]
rs10149435	0.96[EUR][1000 genomes]
rs10438127	0.96[EUR][1000 genomes]
rs1047556	0.97[EUR][1000 genomes]
rs1109170	0.81[CEU][hapmap];0.90[TSI][hapmap]
rs11621351	0.96[EUR][1000 genomes]
rs11622740	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs11625001	0.81[CEU][hapmap]
rs11628437	0.81[CEU][hapmap]
rs15870	0.97[EUR][1000 genomes]
rs17128183	0.91[EUR][1000 genomes]
rs17740741	0.88[CEU][hapmap]
rs17832359	0.96[EUR][1000 genomes]
rs1815316	0.97[EUR][1000 genomes]
rs2075601	0.89[CEU][hapmap];0.95[TSI][hapmap];0.94[EUR][1000 genomes]
rs2075602	0.89[CEU][hapmap];0.95[TSI][hapmap];0.94[EUR][1000 genomes]
rs2075603	1.00[CEU][hapmap];0.82[CHB][hapmap];0.96[EUR][1000 genomes]
rs2094102	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2147972	0.96[EUR][1000 genomes]
rs2274273	1.00[CEU][hapmap];0.82[CHB][hapmap];0.95[TSI][hapmap]
rs2296489	0.82[CHB][hapmap]
rs2340931	0.96[CEU][hapmap];0.98[EUR][1000 genomes]
rs2341622	0.90[TSI][hapmap]
rs28429419	0.93[EUR][1000 genomes]
rs3818451	0.85[CEU][hapmap];0.85[EUR][1000 genomes]
rs3825613	1.00[CEU][hapmap];0.82[CHB][hapmap];0.92[TSI][hapmap];0.96[EUR][1000 genomes]
rs4644	0.96[CEU][hapmap];0.82[CHB][hapmap];0.92[TSI][hapmap];0.95[EUR][1000 genomes]
rs4652	0.84[CEU][hapmap];0.95[TSI][hapmap];0.92[EUR][1000 genomes]
rs56660630	0.88[EUR][1000 genomes]
rs57970196	0.96[EUR][1000 genomes]
rs60972460	0.81[EUR][1000 genomes]
rs61508494	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6573005	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6573006	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6573007	0.94[EUR][1000 genomes]
rs6573009	0.81[CEU][hapmap];0.92[TSI][hapmap]
rs6573013	0.90[TSI][hapmap]
rs6573014	0.90[TSI][hapmap]
rs6573017	0.81[CEU][hapmap]
rs66871576	0.96[EUR][1000 genomes]
rs67098772	0.96[EUR][1000 genomes]
rs67756714	0.96[EUR][1000 genomes]
rs67805055	0.96[EUR][1000 genomes]
rs7140872	0.97[EUR][1000 genomes]
rs7142704	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7147106	0.87[EUR][1000 genomes]
rs7158768	0.81[CEU][hapmap];0.90[TSI][hapmap]
rs7159808	0.89[CEU][hapmap];0.94[EUR][1000 genomes]
rs7160110	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7160523	0.89[CEU][hapmap];0.95[TSI][hapmap];0.94[EUR][1000 genomes]
rs72718804	0.94[EUR][1000 genomes]
rs7493394	0.97[EUR][1000 genomes]
rs8004787	0.88[CEU][hapmap];0.94[EUR][1000 genomes]
rs8007614	0.89[CEU][hapmap];0.86[EUR][1000 genomes]
rs8007620	0.89[CEU][hapmap];0.87[EUR][1000 genomes]
rs8007944	0.92[EUR][1000 genomes]
rs8009670	0.89[CEU][hapmap];0.93[EUR][1000 genomes]
rs8011834	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8012397	0.88[ASW][hapmap]
rs8013027	0.88[CEU][hapmap];0.94[EUR][1000 genomes]
rs8018110	0.90[EUR][1000 genomes]
rs8021583	0.81[CEU][hapmap]
rs8023197	0.81[CEU][hapmap]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1009977	RP11-665C16.6	cis	Muscle Skeletal	GTEx

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:55595400-55606200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr14:55596200-55603200	Transcr. at gene 5' and 3'	Fetal Intestine Small	intestine
3	chr14:55596600-55606400	Transcr. at gene 5' and 3'	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr14:55597000-55613000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr14:55597200-55603600	Weak transcription	HUVEC	blood vessel
6	chr14:55597200-55604000	Weak transcription	Aorta	Aorta
7	chr14:55597200-55604200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr14:55597200-55604600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr14:55597200-55604800	Weak transcription	GM12878-XiMat	blood
10	chr14:55597200-55605200	Weak transcription	A549	lung
11	chr14:55597200-55606600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr14:55597200-55607400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr14:55597400-55603600	Weak transcription	Fetal Lung	lung
14	chr14:55597800-55603600	Weak transcription	Fetal Stomach	stomach
15	chr14:55598400-55607600	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr14:55598400-55613000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr14:55598600-55603600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr14:55598600-55607800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
19	chr14:55598600-55656600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr14:55598800-55603600	Weak transcription	Fetal Muscle Leg	muscle
21	chr14:55598800-55603600	Weak transcription	Placenta	Placenta
22	chr14:55598800-55603600	Weak transcription	Spleen	Spleen
23	chr14:55598800-55605200	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr14:55598800-55605800	Weak transcription	HepG2	liver
25	chr14:55598800-55606000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr14:55598800-55606600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr14:55598800-55610800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
28	chr14:55598800-55611800	Weak transcription	Primary T cells fromperipheralblood	blood
29	chr14:55598800-55613000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
30	chr14:55599200-55604000	Weak transcription	Fetal Thymus	thymus
31	chr14:55599200-55605000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
32	chr14:55599200-55607600	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr14:55599600-55604800	Strong transcription	Primary monocytes fromperipheralblood	blood
34	chr14:55599600-55606400	Weak transcription	Dnd41	blood
35	chr14:55600000-55603800	Enhancers	Skeletal Muscle Male	skeletal muscle
36	chr14:55600200-55604800	Strong transcription	Monocytes-CD14+_RO01746	blood
37	chr14:55600200-55605200	Weak transcription	HUES64 Cell Line	embryonic stem cell
38	chr14:55600200-55613200	Weak transcription	Psoas Muscle	Psoas
39	chr14:55600400-55603600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr14:55600400-55603800	Weak transcription	K562	blood
41	chr14:55600600-55611600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr14:55600800-55609400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
43	chr14:55601000-55604600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
44	chr14:55601200-55603600	Genic enhancers	Rectal Mucosa Donor 31	rectum
45	chr14:55601200-55603600	Weak transcription	Skeletal Muscle Female	skeletal muscle
46	chr14:55601200-55605000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr14:55601600-55603200	Genic enhancers	Rectal Mucosa Donor 29	rectum
48	chr14:55601600-55607000	Weak transcription	HUES48 Cell Line	embryonic stem cell
49	chr14:55601600-55610800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr14:55601800-55603200	Enhancers	Adipose Nuclei	Adipose

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