Variant report

Variant	rs6464937
Chromosome Location	chr7:140372579-140372580
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	chr7:140372380-140373159	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr7:140372526-140373472	H1-neurons	neurons:	n/a	n/a
3	MAX	chr7:140372431-140373722	H1-hESC	embryonic stem cell:	n/a	chr7:140372802-140372812 chr7:140372990-140373000
4	YY1	chr7:140372455-140372699	ECC-1	luminal epithelium:	n/a	chr7:140372490-140372502
5	POLR2A	chr7:140372420-140373536	GM12878	blood:	n/a	n/a
6	POLR2A	chr7:140372433-140373614	HCT-116	colon:	n/a	n/a
7	POLR2A	chr7:140372503-140372629	H1-hESC	embryonic stem cell:	n/a	n/a
8	POLR2A	chr7:140372447-140373749	HEK293	kidney:	n/a	n/a
9	POLR2A	chr7:140372572-140373509	K562	blood:	n/a	n/a
10	E2F6	chr7:140372447-140373554	K562	blood:	n/a	chr7:140372848-140372858 chr7:140372998-140373013
11	MAZ	chr7:140372359-140373651	GM12878	blood:	n/a	chr7:140372802-140372812 chr7:140372990-140373000
12	ELF1	chr7:140372574-140374124	GM12878	blood:	n/a	chr7:140372797-140372809
13	POLR2A	chr7:140372427-140373802	MCF-7	breast:	n/a	n/a
14	ZEB1	chr7:140372503-140374016	GM12878	blood:	n/a	n/a
15	CTCF	chr7:140372542-140372610	H1-hESC	embryonic stem cell:	n/a	chr7:140372556-140372563
16	MAZ	chr7:140372063-140373834	K562	blood:	n/a	chr7:140372802-140372812 chr7:140372990-140373000
17	RUNX3	chr7:140372420-140372655	GM12878	blood:	n/a	n/a
18	POLR2A	chr7:140372437-140373543	GM12878	blood:	n/a	n/a
19	NR2F2	chr7:140372507-140373810	MCF-7	breast:	n/a	n/a
20	TCF12	chr7:140372488-140372662	H1-hESC	embryonic stem cell:	n/a	n/a
21	ZBTB7A	chr7:140372495-140373469	K562	blood:	n/a	n/a
22	MYC	chr7:140372576-140373625	K562	blood:	n/a	chr7:140372802-140372812 chr7:140372990-140373000
23	MAX	chr7:140372457-140373758	MCF-7	breast:	n/a	chr7:140372802-140372812 chr7:140372990-140373000
24	POLR2A	chr7:140372491-140372639	Hela-S3	cervix:	n/a	n/a
25	POLR2A	chr7:140372402-140373583	GM12892	blood:	n/a	n/a
26	TAF1	chr7:140372453-140373594	ECC-1	luminal epithelium:	n/a	n/a
27	POLR2A	chr7:140372379-140374681	Raji	blood:	n/a	n/a
28	YY1	chr7:140372365-140372635	H1-hESC	embryonic stem cell:	n/a	chr7:140372490-140372502
29	CTCF	chr7:140372520-140372670	GM12867	blood:	n/a	chr7:140372556-140372563
30	YY1	chr7:140372435-140372689	GM12891	blood:	n/a	chr7:140372490-140372502
31	HMGN3	chr7:140372473-140373679	K562	blood:	n/a	n/a
32	MAX	chr7:140372473-140373726	ECC-1	luminal epithelium:	n/a	chr7:140372802-140372812 chr7:140372990-140373000
33	MAX	chr7:140372518-140373519	A549	lung:	n/a	chr7:140372802-140372812 chr7:140372990-140373000
34	POLR2A	chr7:140372551-140373386	HepG2	liver:	n/a	n/a
35	POLR2A	chr7:140372436-140373657	HCT-116	colon:	n/a	n/a
36	MAX	chr7:140372534-140373468	HepG2	liver:	n/a	chr7:140372802-140372812 chr7:140372990-140373000
37	CTCF	chr7:140372480-140372630	HEK293	kidney:	n/a	chr7:140372556-140372563
38	YY1	chr7:140372484-140372648	K562	blood:	n/a	chr7:140372490-140372502
39	MAX	chr7:140372430-140373471	ECC-1	luminal epithelium:	n/a	chr7:140372802-140372812 chr7:140372990-140373000
40	POLR2A	chr7:140372504-140373525	A549	lung:	n/a	n/a
41	POLR2A	chr7:140372425-140373584	GM18526	blood:	n/a	n/a
42	POLR2A	chr7:140372402-140373630	GM12891	blood:	n/a	n/a
43	POLR2A	chr7:140372503-140372640	A549	lung:	n/a	n/a
44	POLR2A	chr7:140372504-140373776	MCF-7	breast:	n/a	n/a
45	MYC	chr7:140372563-140372956	MCF-7	breast:	n/a	chr7:140372802-140372812
46	HEY1	chr7:140372536-140372970	HepG2	liver:	n/a	chr7:140372788-140372803 chr7:140372809-140372824
47	POLR2A	chr7:140372513-140373370	HepG2	liver:	n/a	n/a
48	E2F6	chr7:140372484-140372832	H1-hESC	embryonic stem cell:	n/a	n/a
49	MAX	chr7:140372509-140373710	A549	lung:	n/a	chr7:140372802-140372812 chr7:140372990-140373000
50	POLR2A	chr7:140372510-140374150	GM19193	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr7:140370608..140383131-chr7:140387718..140398587,28	MCF-7	breast:
2	chr7:140371506..140376729-chr7:140377280..140380130,6	K562	blood:
3	chr7:140371233..140372859-chr7:140417535..140420248,2	MCF-7	breast:
4	chr7:140371560..140374067-chr7:140396511..140398663,2	K562	blood:
5	chr7:140371193..140374993-chr7:140376654..140380151,6	MCF-7	breast:
6	chr7:140358444..140360553-chr7:140370671..140372780,2	MCF-7	breast:
7	chr7:140366280..140367939-chr7:140371289..140372844,2	MCF-7	breast:
8	chr7:140370275..140375389-chr7:140393210..140401279,16	MCF-7	breast:

Variant related genes	Relation type
ADCK2	TF binding region
ENSG00000240889	Chromatin interaction
ENSG00000133597	Chromatin interaction
ENSG00000090266	Chromatin interaction

Extended variants
information (count: 68 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10228254	0.85[ASN][1000 genomes]
rs10241711	0.83[CHB][hapmap]
rs10258462	0.85[ASN][1000 genomes]
rs10258465	0.85[ASN][1000 genomes]
rs10260676	0.83[ASN][1000 genomes]
rs1046515	0.81[CHB][hapmap]
rs1140034	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12375245	0.83[CHB][hapmap];0.81[ASN][1000 genomes]
rs1267600	0.91[CHB][hapmap]
rs1267601	0.91[CHB][hapmap]
rs1267606	0.91[CHB][hapmap]
rs1267611	0.81[CHB][hapmap]
rs1267613	0.81[CHB][hapmap]
rs1267619	0.91[CHB][hapmap]
rs1267636	0.81[CHB][hapmap]
rs1267638	0.91[CHB][hapmap]
rs1267642	0.81[CHB][hapmap]
rs1267643	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs1267644	0.81[CHB][hapmap]
rs1267649	0.91[CHB][hapmap]
rs1639675	0.91[CHB][hapmap]
rs1639678	0.91[CHB][hapmap]
rs1639679	0.81[CHB][hapmap]
rs17161666	0.83[CHB][hapmap]
rs17161668	0.81[ASN][1000 genomes]
rs17161750	0.91[CHB][hapmap]
rs1733827	0.91[CHB][hapmap]
rs1733832	0.91[CHB][hapmap]
rs2364393	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2364394	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2364395	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2364396	0.83[CHB][hapmap]
rs2364397	1.00[ASW][hapmap];0.83[CHB][hapmap];0.81[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.93[MKK][hapmap];0.81[ASN][1000 genomes]
rs2364399	0.80[MKK][hapmap]
rs2535951	0.91[CHB][hapmap]
rs28517771	0.90[ASN][1000 genomes]
rs2907950	0.89[ASN][1000 genomes]
rs2930315	0.84[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs2930318	0.94[ASN][1000 genomes]
rs2930319	0.84[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs2930328	0.89[MKK][hapmap]
rs2930329	0.89[MKK][hapmap]
rs2930331	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2968549	0.87[ASN][1000 genomes]
rs2968550	1.00[ASW][hapmap];0.83[CHB][hapmap];0.81[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.94[MKK][hapmap];0.87[ASN][1000 genomes]
rs2968551	0.92[ASN][1000 genomes]
rs2968553	1.00[ASW][hapmap];0.83[CHB][hapmap];0.81[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.94[MKK][hapmap];0.84[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs2968555	0.96[ASN][1000 genomes]
rs2968558	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2968559	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4624945	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4725799	0.81[ASN][1000 genomes]
rs4727011	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4727021	0.81[ASN][1000 genomes]
rs4727036	0.81[ASN][1000 genomes]
rs4727040	0.83[CHB][hapmap]
rs4727041	0.83[CHB][hapmap]
rs6464036	0.91[CHB][hapmap]
rs6464123	0.91[CHB][hapmap]
rs6977834	0.87[ASN][1000 genomes]
rs73505645	0.90[ASN][1000 genomes]
rs73505647	0.88[ASN][1000 genomes]
rs7792746	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs7794857	0.85[ASN][1000 genomes]
rs7803697	1.00[ASW][hapmap];0.83[CHB][hapmap];0.81[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.94[MKK][hapmap];0.87[ASN][1000 genomes]
rs7809339	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831157	chr7:140241339-140426876	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	esv3373922	chr7:140371933-140374031	Active TSS Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	n/a

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6464937	ADCK2	Cis_1M	lymphoblastoid	RTeQTL
rs6464937	DGKI	cis	cerebellum	SCAN
rs6464937	TMEM139	cis	parietal	SCAN
rs6464937	NDUFB2	cis	lymphoblastoid	seeQTL

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:140372000-140372600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr7:140372000-140372600	Flanking Active TSS	Fetal Kidney	kidney
3	chr7:140372000-140372600	Flanking Active TSS	Hela-S3	cervix
4	chr7:140372000-140372600	Flanking Active TSS	K562	blood
5	chr7:140372000-140372800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
6	chr7:140372000-140372800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr7:140372000-140373000	Active TSS	HUES64 Cell Line	embryonic stem cell
8	chr7:140372000-140373200	Active TSS	Brain Hippocampus Middle	brain
9	chr7:140372000-140373400	Active TSS	Primary T helper naive cells from peripheral blood	blood
10	chr7:140372200-140372600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr7:140372200-140372600	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
12	chr7:140372200-140372600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
13	chr7:140372200-140372600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
14	chr7:140372200-140372600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
15	chr7:140372200-140372600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
16	chr7:140372200-140372600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr7:140372200-140372600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr7:140372200-140372600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr7:140372200-140372600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr7:140372200-140372600	Flanking Active TSS	Adipose Nuclei	Adipose
21	chr7:140372200-140372600	Flanking Active TSS	Fetal Brain Male	brain
22	chr7:140372200-140372600	Flanking Active TSS	Fetal Muscle Leg	muscle
23	chr7:140372200-140372600	Flanking Active TSS	Rectal Smooth Muscle	rectum
24	chr7:140372200-140372600	Flanking Active TSS	Dnd41	blood
25	chr7:140372200-140372600	Flanking Active TSS	HepG2	liver
26	chr7:140372200-140372600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
27	chr7:140372200-140372800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr7:140372200-140372800	Active TSS	Primary hematopoietic stem cells short term culture	blood
29	chr7:140372200-140372800	Weak transcription	Spleen	Spleen
30	chr7:140372200-140373000	Active TSS	ES-I3 Cell Line	embryonic stem cell
31	chr7:140372200-140373000	Active TSS	Liver	Liver
32	chr7:140372200-140373000	Active TSS	Skeletal Muscle Male	skeletal muscle
33	chr7:140372200-140373000	Active TSS	Stomach Smooth Muscle	stomach
34	chr7:140372200-140373200	Active TSS	H1 Cell Line	embryonic stem cell
35	chr7:140372200-140373200	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr7:140372200-140373200	Active TSS	Muscle Satellite Cultured Cells	--
37	chr7:140372200-140373200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr7:140372200-140373200	Active TSS	GM12878-XiMat	blood
39	chr7:140372200-140373400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr7:140372200-140373400	Active TSS	Primary T killer naive cells fromperipheralblood	blood
41	chr7:140372200-140373400	Active TSS	Brain Inferior Temporal Lobe	brain
42	chr7:140372200-140373400	Active TSS	Fetal Brain Female	brain
43	chr7:140372200-140373400	Active TSS	Placenta	Placenta
44	chr7:140372200-140373400	Active TSS	Right Atrium	heart
45	chr7:140372200-140373600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr7:140372200-140373600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr7:140372200-140373600	Active TSS	Brain Angular Gyrus	brain
48	chr7:140372200-140373800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr7:140372200-140373800	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr7:140372200-140374000	Active TSS	Duodenum Smooth Muscle	Duodenum

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