Variant report

Variant	rs7317852
Chromosome Location	chr13:39611148-39611149
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	MAX	chr13:39610127-39614057	NB4	blood:	n/a	chr13:39610504-39610514 chr13:39610831-39610839
2	SIN3A	chr13:39610440-39613140	H1-hESC	embryonic stem cell:	n/a	chr13:39611723-39611734
3	CEBPB	chr13:39610469-39611186	K562	blood:	n/a	n/a
4	REST	chr13:39610990-39613180	H1-neurons	neurons:	n/a	chr13:39611826-39611839 chr13:39611712-39611730 chr13:39611438-39611451 chr13:39612005-39612025
5	CEBPB	chr13:39610395-39611322	Hela-S3	cervix:	n/a	chr13:39611221-39611232
6	POLR2A	chr13:39610255-39611362	K562	blood:	n/a	n/a
7	HCFC1	chr13:39610797-39613004	Hela-S3	cervix:	n/a	n/a
8	POLR2A	chr13:39611086-39613293	H1-hESC	embryonic stem cell:	n/a	n/a
9	MYC	chr13:39610008-39613668	NB4	blood:	n/a	chr13:39610504-39610514 chr13:39610831-39610839
10	ZNF263	chr13:39610456-39613037	HEK293-T-REx	kidney:	n/a	chr13:39612043-39612064
11	POLR2A	chr13:39610318-39613025	MCF10A-Er-Src	breast:	n/a	n/a
12	CHD1	chr13:39610173-39612535	H1-hESC	embryonic stem cell:	n/a	n/a
13	E2F4	chr13:39610898-39611209	MCF10A-Er-Src	breast:	n/a	chr13:39610917-39610926
14	MXI1	chr13:39610320-39611300	GM12878	blood:	n/a	n/a
15	MXI1	chr13:39610404-39611325	Hela-S3	cervix:	n/a	n/a
16	POLR2A	chr13:39611036-39613133	Hela-S3	cervix:	n/a	n/a
17	MYC	chr13:39609509-39611304	MCF10A-Er-Src	breast:	n/a	chr13:39610504-39610514 chr13:39610831-39610839
18	POLR2A	chr13:39610377-39613654	GM12891	blood:	n/a	n/a
19	POLR2A	chr13:39611072-39613157	MCF10A-Er-Src	breast:	n/a	n/a
20	STAT3	chr13:39610411-39611309	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr13:39610419..39613692-chr13:39616080..39618520,4	K562	blood:
2	chr13:39600178..39602849-chr13:39610760..39613364,3	K562	blood:
3	chr13:39596727..39599413-chr13:39610585..39613126,4	MCF-7	breast:

Variant related genes	Relation type
NHLRC3	TF binding region
ENSG00000120685	Chromatin interaction
ENSG00000188811	Chromatin interaction

Extended variants
information (count: 81 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs1109625	1.00[CEU][hapmap]
rs11147745	0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs12428445	0.92[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs12429324	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs12429338	0.96[ASN][1000 genomes]
rs12430450	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs12431316	0.87[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs1326405	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17058947	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs17058990	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17059014	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2094252	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2094253	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2094254	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2104518	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2274384	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.94[TSI][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2274385	0.92[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs2296648	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs34316151	0.95[ASN][1000 genomes]
rs34327528	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35804724	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35864330	0.87[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs3751377	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.91[MKK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs3751378	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.91[MKK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs3751379	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs3812879	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs4142398	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55809136	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66496062	0.89[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs66908302	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs67296293	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73169457	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7318688	1.00[ASN][1000 genomes]
rs7327748	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs747752	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs7987207	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.92[YRI][hapmap];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7994530	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7997052	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.92[YRI][hapmap];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7998475	0.95[ASN][1000 genomes]
rs8000929	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9566385	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9566389	0.89[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs9566391	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9566393	0.90[ASN][1000 genomes]
rs9566396	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9566397	0.82[ASN][1000 genomes]
rs9576666	1.00[CEU][hapmap]
rs9576669	1.00[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];0.80[CHD][hapmap];0.85[GIH][hapmap];0.92[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9576670	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9576673	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9576674	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9576676	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9576677	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9576678	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9576679	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9576681	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9576683	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9576684	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9576685	0.95[ASN][1000 genomes]
rs9576686	0.87[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs9576688	0.95[ASN][1000 genomes]
rs9576690	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9576691	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9576692	0.89[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs9576693	0.93[ASN][1000 genomes]
rs9576695	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9576696	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9576697	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs9576698	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs9576699	1.00[CHB][hapmap];0.89[JPT][hapmap];0.96[ASN][1000 genomes]
rs9576700	0.96[ASN][1000 genomes]
rs9576701	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9576703	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9576705	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9576707	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9576710	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];0.92[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.94[TSI][hapmap];0.92[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9576711	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.94[TSI][hapmap];0.92[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9576717	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[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	esv2754118	chr13:39347702-40222644	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	esv2753642	chr13:39522300-39649000	Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases
3	esv2753553	chr13:39526600-39649000	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7317852	LHFP	cis	cerebellum	SCAN
rs7317852	C13orf23	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:39599800-39611200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr13:39608800-39611200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr13:39609000-39611400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr13:39609000-39615000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr13:39609000-39615200	Active TSS	K562	blood
6	chr13:39609200-39613600	Active TSS	ES-I3 Cell Line	embryonic stem cell
7	chr13:39609200-39613800	Active TSS	GM12878-XiMat	blood
8	chr13:39609400-39611200	Flanking Active TSS	Primary hematopoietic stem cells	blood
9	chr13:39609400-39611200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr13:39609400-39611200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
11	chr13:39609400-39611200	Flanking Active TSS	HUVEC	blood vessel
12	chr13:39609400-39611400	Flanking Active TSS	Primary T cells from cord blood	blood
13	chr13:39609400-39611400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
14	chr13:39609400-39611400	Flanking Active TSS	Liver	Liver
15	chr13:39609400-39611400	Flanking Active TSS	Brain Anterior Caudate	brain
16	chr13:39609400-39611600	Flanking Active TSS	Adipose Nuclei	Adipose
17	chr13:39609400-39611600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
18	chr13:39609400-39611800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
19	chr13:39609400-39613200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr13:39609400-39613400	Active TSS	iPS-15b Cell Line	embryonic stem cell
21	chr13:39609400-39613400	Active TSS	NHLF	lung
22	chr13:39609400-39613800	Active TSS	HUES6 Cell Line	embryonic stem cell
23	chr13:39609400-39613800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr13:39609600-39611200	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
25	chr13:39609600-39611400	Weak transcription	Spleen	Spleen
26	chr13:39609600-39611800	Flanking Active TSS	Primary B cells from cord blood	blood
27	chr13:39609600-39612600	Active TSS	HMEC	breast
28	chr13:39609600-39613000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
29	chr13:39609600-39613200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr13:39609600-39613400	Active TSS	H9 Cell Line	embryonic stem cell
31	chr13:39609600-39613400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr13:39609600-39613400	Active TSS	Aorta	Aorta
33	chr13:39609600-39613400	Active TSS	Colon Smooth Muscle	Colon
34	chr13:39609600-39613400	Active TSS	Psoas Muscle	Psoas
35	chr13:39609600-39613400	Active TSS	Stomach Smooth Muscle	stomach
36	chr13:39609600-39613400	Active TSS	HSMMtube	muscle
37	chr13:39609600-39613600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr13:39609600-39613600	Active TSS	Ovary	ovary
39	chr13:39609600-39613600	Active TSS	Right Atrium	heart
40	chr13:39609600-39613600	Active TSS	Right Ventricle	heart
41	chr13:39609600-39613800	Active TSS	Fetal Muscle Leg	muscle
42	chr13:39609600-39613800	Active TSS	NHEK	skin
43	chr13:39609600-39614000	Active TSS	Hela-S3	cervix
44	chr13:39609600-39614200	Active TSS	Fetal Intestine Large	intestine
45	chr13:39609600-39614800	Active TSS	Placenta	Placenta
46	chr13:39609800-39613200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr13:39609800-39613400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr13:39609800-39613400	Active TSS	HSMM	muscle
49	chr13:39609800-39613600	Active TSS	H1 Cell Line	embryonic stem cell
50	chr13:39609800-39613600	Active TSS	Fetal Thymus	thymus

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