Variant report

Variant	rs12127879
Chromosome Location	chr1:246172162-246172163
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:246171457..246174001-chr1:246174908..246177253,2	K562	blood:

Extended variants
information (count: 95 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10802330	1.00[CEU][hapmap];1.00[ASN][1000 genomes]
rs10802331	1.00[ASN][1000 genomes]
rs10924447	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10924451	1.00[ASN][1000 genomes]
rs10924452	1.00[ASN][1000 genomes]
rs10924455	1.00[CEU][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10924471	1.00[CEU][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10924493	1.00[CEU][hapmap];1.00[ASN][1000 genomes]
rs10924497	1.00[ASN][1000 genomes]
rs12063211	1.00[CEU][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12063317	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12074800	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12080754	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12085648	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12089263	1.00[CEU][hapmap];1.00[ASN][1000 genomes]
rs12094046	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12094672	1.00[CEU][hapmap];1.00[ASN][1000 genomes]
rs12094677	1.00[ASN][1000 genomes]
rs12098007	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12118507	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12121282	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12122251	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12122288	1.00[CEU][hapmap];1.00[ASN][1000 genomes]
rs12124651	1.00[ASN][1000 genomes]
rs12128271	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12128549	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12128668	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12129767	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12130360	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12131368	1.00[CEU][hapmap];1.00[ASN][1000 genomes]
rs12135913	1.00[ASN][1000 genomes]
rs12143713	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12145214	1.00[ASN][1000 genomes]
rs12145610	1.00[CEU][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12354335	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12724208	1.00[ASN][1000 genomes]
rs13376689	1.00[ASN][1000 genomes]
rs28642395	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4417031	1.00[CEU][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55636411	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56041192	1.00[ASN][1000 genomes]
rs57769476	1.00[ASN][1000 genomes]
rs58870979	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61572151	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6426261	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6657610	1.00[ASN][1000 genomes]
rs6661444	1.00[ASN][1000 genomes]
rs6675531	1.00[ASN][1000 genomes]
rs6690727	1.00[CEU][hapmap]
rs6695318	1.00[ASN][1000 genomes]
rs73133756	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73137854	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73137858	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73137902	1.00[ASN][1000 genomes]
rs74154349	1.00[ASN][1000 genomes]
rs74154351	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74154354	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74154355	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74154363	1.00[ASN][1000 genomes]
rs74154369	1.00[ASN][1000 genomes]
rs74154370	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:34 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	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
16	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
17	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
18	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
19	nsv1007245	chr1:246120132-246619260	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
20	nsv535395	chr1:246120132-246619260	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
21	nsv1001139	chr1:246120516-246548942	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
22	nsv873408	chr1:246122871-246187900	Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
23	nsv873409	chr1:246122871-246429058	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
24	nsv430402	chr1:246124959-246787448	Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
25	nsv549524	chr1:246127777-246391677	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
26	nsv1005717	chr1:246141553-246207278	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
27	nsv535396	chr1:246141553-246207278	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
28	nsv549526	chr1:246142250-246293716	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
29	nsv497890	chr1:246143172-246778453	Enhancers Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
30	nsv1005310	chr1:246151590-246666101	Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
31	nsv1003239	chr1:246166737-246666101	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
32	nsv535397	chr1:246166737-246666101	Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
33	nsv998930	chr1:246166737-246702012	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
34	nsv526469	chr1:246168017-246490438	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:246163800-246175400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr1:246163800-246175800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr1:246169000-246175800	Weak transcription	Colon Smooth Muscle	Colon
4	chr1:246169000-246176000	Weak transcription	Fetal Stomach	stomach
5	chr1:246169200-246175200	Weak transcription	K562	blood
6	chr1:246170600-246175800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
7	chr1:246171200-246172600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr1:246171400-246172200	Enhancers	HUES6 Cell Line	embryonic stem cell
9	chr1:246171400-246172200	Enhancers	Duodenum Mucosa	Duodenum
10	chr1:246171400-246172600	Enhancers	Stomach Mucosa	stomach
11	chr1:246171600-246172200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr1:246171600-246172200	Active TSS	Brain Angular Gyrus	brain
13	chr1:246171600-246172200	Active TSS	Brain Inferior Temporal Lobe	brain
14	chr1:246171600-246172200	Flanking Active TSS	Brain Substantia Nigra	brain
15	chr1:246171600-246172200	Enhancers	Fetal Kidney	kidney
16	chr1:246171600-246172200	Flanking Active TSS	Ovary	ovary
17	chr1:246171600-246172200	Enhancers	Rectal Mucosa Donor 31	rectum
18	chr1:246171600-246172400	Enhancers	H1 Cell Line	embryonic stem cell
19	chr1:246171600-246172400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr1:246171600-246172400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr1:246171600-246172400	Flanking Active TSS	Brain Cingulate Gyrus	brain
22	chr1:246171800-246172200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
23	chr1:246171800-246172200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr1:246171800-246172200	Active TSS	Brain Anterior Caudate	brain
25	chr1:246171800-246172200	Active TSS	Brain Hippocampus Middle	brain
26	chr1:246171800-246172200	Flanking Active TSS	Placenta	Placenta
27	chr1:246171800-246172200	Flanking Active TSS	HMEC	breast
28	chr1:246171800-246172400	Active TSS	Breast Myoepithelial Primary Cells	Breast
29	chr1:246172000-246172200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr1:246172000-246172200	Flanking Active TSS	NHEK	skin
31	chr1:246172000-246172600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links