Variant report

Variant	rs4142898
Chromosome Location	chr1:246117191-246117192
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:246114942..246117508-chr1:246123579..246126563,3	K562	blood:
2	chr1:246115282..246117268-chr20:9203309..9206054,2	MCF-7	breast:
3	chr1:246115508..246118574-chr1:246120452..246123477,3	K562	blood:

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10754490	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10924394	0.81[EUR][1000 genomes]
rs10924396	0.89[GIH][hapmap];0.83[EUR][1000 genomes]
rs10924399	0.89[GIH][hapmap];0.83[TSI][hapmap];0.83[EUR][1000 genomes]
rs10924400	0.83[EUR][1000 genomes]
rs11578625	0.80[EUR][1000 genomes]
rs12064270	0.83[EUR][1000 genomes]
rs12093398	0.82[CEU][hapmap];0.89[GIH][hapmap];0.87[EUR][1000 genomes]
rs55974833	0.83[EUR][1000 genomes]
rs6685357	1.00[CEU][hapmap];0.94[GIH][hapmap];0.89[LWK][hapmap];0.81[TSI][hapmap];0.87[YRI][hapmap];0.84[AFR][1000 genomes];0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:32 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007728	chr1:245235174-246156455	Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Enhancers Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
2	nsv497871	chr1:245706209-246655353	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	nsv534412	chr1:245747724-246655416	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv1003594	chr1:245801793-246649329	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
5	nsv1004412	chr1:245830921-246169054	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv535385	chr1:245830921-246169054	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	nsv998801	chr1:245924108-246131115	Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv535386	chr1:245924108-246131115	Active TSS Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv1014841	chr1:245936464-246143222	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv535387	chr1:245936464-246143222	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
11	nsv1008786	chr1:245948622-246514454	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
12	nsv535388	chr1:245948622-246514454	Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
13	nsv468805	chr1:245950642-246229245	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
14	nsv549521	chr1:245950642-246229245	Enhancers ZNF genes & repeats Weak transcription Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
15	nsv1004119	chr1:245957145-246813150	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
16	nsv535389	chr1:245957145-246813150	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
17	nsv1014529	chr1:245957145-246817877	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
18	nsv1000654	chr1:245966390-246778182	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
19	nsv535392	chr1:245966390-246778182	Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
20	nsv868852	chr1:245969229-246811220	Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
21	nsv1005074	chr1:245999762-246141613	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
22	nsv1013699	chr1:246005308-246143361	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
23	nsv535393	chr1:246005308-246143361	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
24	nsv1003768	chr1:246024121-246169054	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
25	nsv1014150	chr1:246038971-246208095	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
26	nsv1003627	chr1:246051016-246352723	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
27	nsv535394	chr1:246051016-246352723	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
28	esv3399499	chr1:246074488-246122311	Enhancers Strong transcription Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
29	nsv1013841	chr1:246080712-246317730	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
30	nsv948348	chr1:246090818-246853200	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
31	nsv873407	chr1:246106084-246148791	Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
32	nsv1002445	chr1:246112327-246129652	Flanking Active TSS Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:246103800-246132600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr1:246112400-246117400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr1:246112400-246117600	Weak transcription	Lung	lung
4	chr1:246112600-246117600	Weak transcription	Pancreas	Pancrea
5	chr1:246112600-246117800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr1:246112600-246127400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr1:246112600-246132000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr1:246115600-246117200	Flanking Active TSS	GM12878-XiMat	blood
9	chr1:246116200-246117600	Weak transcription	Spleen	Spleen
10	chr1:246116400-246117600	Active TSS	Duodenum Mucosa	Duodenum
11	chr1:246116400-246118200	Enhancers	HUES64 Cell Line	embryonic stem cell
12	chr1:246116600-246117200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
13	chr1:246116600-246117600	Active TSS	Primary T helper cells PMA-I stimulated	--
14	chr1:246116600-246117800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr1:246116600-246117800	Active TSS	Brain Hippocampus Middle	brain
16	chr1:246116600-246118000	Active TSS	Brain Inferior Temporal Lobe	brain
17	chr1:246116600-246118000	Active TSS	Stomach Smooth Muscle	stomach
18	chr1:246116600-246118200	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
19	chr1:246116600-246118200	Enhancers	Fetal Thymus	thymus
20	chr1:246116800-246117200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
21	chr1:246116800-246117200	Enhancers	Primary hematopoietic stem cells short term culture	blood
22	chr1:246116800-246117200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
23	chr1:246116800-246117200	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
24	chr1:246116800-246117200	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
25	chr1:246116800-246117200	Flanking Active TSS	HSMM	muscle
26	chr1:246116800-246117600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr1:246116800-246117600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr1:246116800-246117600	Active TSS	Primary T cells from cord blood	blood
29	chr1:246116800-246117600	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
30	chr1:246116800-246117600	Active TSS	Primary T helper naive cells fromperipheralblood	blood
31	chr1:246116800-246117600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr1:246116800-246117600	Active TSS	Liver	Liver
33	chr1:246116800-246117600	Active TSS	Brain Substantia Nigra	brain
34	chr1:246116800-246117600	Active TSS	Rectal Mucosa Donor 29	rectum
35	chr1:246116800-246117600	Active TSS	Rectal Mucosa Donor 31	rectum
36	chr1:246116800-246117600	Active TSS	Skeletal Muscle Female	skeletal muscle
37	chr1:246116800-246117800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr1:246116800-246117800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr1:246116800-246117800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr1:246116800-246117800	Active TSS	Brain Anterior Caudate	brain
41	chr1:246116800-246117800	Active TSS	Ovary	ovary
42	chr1:246116800-246117800	Active TSS	Right Atrium	heart
43	chr1:246116800-246118000	Flanking Active TSS	Adipose Nuclei	Adipose
44	chr1:246116800-246118000	Active TSS	Brain Angular Gyrus	brain
45	chr1:246116800-246118000	Enhancers	Fetal Muscle Leg	muscle
46	chr1:246116800-246118000	Active TSS	Rectal Smooth Muscle	rectum
47	chr1:246116800-246118200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr1:246117000-246117200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr1:246117000-246117200	Flanking Active TSS	Primary B cells from peripheral blood	blood
50	chr1:246117000-246117200	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood

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