Variant report

Variant	rs7605966
Chromosome Location	chr2:39999833-39999834
allele	A/G
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	chr2:39999568-39999863	MCF10A-Er-Src	breast:	n/a	n/a
2	STAT3	chr2:39999663-39999863	MCF10A-Er-Src	breast:	n/a	chr2:39999841-39999855 chr2:39999842-39999853
3	STAT3	chr2:39999749-39999865	MCF10A-Er-Src	breast:	n/a	chr2:39999841-39999855 chr2:39999842-39999853
4	MYC	chr2:39999587-39999862	MCF10A-Er-Src	breast:	n/a	n/a
5	POLR2A	chr2:39999680-40000508	K562	blood:	n/a	n/a
6	FOS	chr2:39999565-39999864	MCF10A-Er-Src	breast:	n/a	chr2:39999734-39999742 chr2:39999735-39999746
7	POLR2A	chr2:39999653-40000070	K562	blood:	n/a	n/a
8	FOS	chr2:39999540-39999912	MCF10A-Er-Src	breast:	n/a	chr2:39999734-39999742 chr2:39999735-39999746
9	FOS	chr2:39999548-39999903	MCF10A-Er-Src	breast:	n/a	chr2:39999734-39999742 chr2:39999735-39999746
10	STAT3	chr2:39999664-39999991	MCF10A-Er-Src	breast:	n/a	chr2:39999841-39999855 chr2:39999842-39999853
11	FOS	chr2:39999566-39999903	MCF10A-Er-Src	breast:	n/a	chr2:39999734-39999742 chr2:39999735-39999746
12	CEBPB	chr2:39999526-39999900	IMR90	lung:	n/a	n/a
13	MXI1	chr2:39999778-39999836	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:39997806..40003955-chr2:40003961..40007756,6	MCF-7	breast:
2	chr2:39909390..39911752-chr2:39999764..40002592,2	K562	blood:
3	chr2:39981401..39983374-chr2:39998682..40001306,2	K562	blood:
4	chr2:39541547..39543631-chr2:39997665..39999926,2	K562	blood:
5	chr2:39999247..40000027-chr6:14903249..14904079,2	MCF-7	breast:

Variant related genes	Relation type
THUMPD2	TF binding region
ENSG00000138050	Chromatin interaction
ENSG00000011566	Chromatin interaction

Extended variants
information (count: 5 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:1)

rs_ID	r²[population]
rs10196026	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833870	chr2:39837022-40026024	Flanking Bivalent TSS/Enh Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv833881	chr2:39914558-40067256	Weak transcription Enhancers Strong transcription Bivalent Enhancer Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv873890	chr2:39976810-40009041	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv2696	chr2:39988381-40033288	Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39965200-40005000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:39965200-40005400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr2:39978600-40000000	Weak transcription	Fetal Heart	heart
4	chr2:39985000-40005000	Weak transcription	Colonic Mucosa	Colon
5	chr2:39985200-40005000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr2:39985400-40005200	Weak transcription	Fetal Brain Male	brain
7	chr2:39985600-40001000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr2:39985800-40004800	Weak transcription	Fetal Brain Female	brain
9	chr2:39985800-40005000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr2:39985800-40005400	Weak transcription	Primary neutrophils fromperipheralblood	blood
11	chr2:39985800-40005400	Weak transcription	Lung	lung
12	chr2:39986000-40004200	Weak transcription	Brain Cingulate Gyrus	brain
13	chr2:39986200-40004400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr2:39987400-40001000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
15	chr2:39987400-40001000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr2:39987600-40001000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr2:39987600-40003200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr2:39988000-40004400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr2:39991200-40000200	Strong transcription	A549	lung
20	chr2:39992000-40004400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr2:39992000-40004600	Weak transcription	Fetal Kidney	kidney
22	chr2:39995400-40000000	Strong transcription	Primary B cells from cord blood	blood
23	chr2:39995400-40000200	Strong transcription	Fetal Thymus	thymus
24	chr2:39996400-40001000	Weak transcription	Rectal Smooth Muscle	rectum
25	chr2:39996400-40004200	Weak transcription	Stomach Smooth Muscle	stomach
26	chr2:39996400-40005000	Weak transcription	Stomach Mucosa	stomach
27	chr2:39996600-40004600	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr2:39997000-40001000	Weak transcription	Pancreas	Pancrea
29	chr2:39997000-40003400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr2:39997000-40003400	Weak transcription	Fetal Intestine Large	intestine
31	chr2:39997000-40004200	Weak transcription	Thymus	Thymus
32	chr2:39997000-40004400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr2:39997000-40004400	Weak transcription	Fetal Stomach	stomach
34	chr2:39997000-40004400	Weak transcription	Rectal Mucosa Donor 29	rectum
35	chr2:39997000-40004800	Weak transcription	Fetal Intestine Small	intestine
36	chr2:39997000-40005200	Weak transcription	Fetal Muscle Trunk	muscle
37	chr2:39997000-40005400	Weak transcription	Placenta	Placenta
38	chr2:39997000-40005800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr2:39997200-40004200	Weak transcription	Duodenum Mucosa	Duodenum
40	chr2:39997600-40003800	Weak transcription	Primary hematopoietic stem cells	blood
41	chr2:39998200-40001000	Weak transcription	Primary T cells fromperipheralblood	blood
42	chr2:39998400-40000200	Enhancers	iPS-15b Cell Line	embryonic stem cell
43	chr2:39998400-40000200	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
44	chr2:39998600-40004400	Weak transcription	Primary B cells from peripheral blood	blood
45	chr2:39998600-40004400	Weak transcription	Liver	Liver
46	chr2:39998800-40000000	Weak transcription	Duodenum Smooth Muscle	Duodenum
47	chr2:39998800-40000400	Enhancers	HMEC	breast
48	chr2:39998800-40004000	Weak transcription	Monocytes-CD14+_RO01746	blood
49	chr2:39999000-40000200	Enhancers	HUES6 Cell Line	embryonic stem cell
50	chr2:39999000-40000200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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