Variant report

Variant	rs56109009
Chromosome Location	chr1:9828323-9828324
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:9821662..9824159-chr1:9828181..9830598,2	K562	blood:
2	chr1:9827688..9830515-chr1:9884401..9886148,2	MCF-7	breast:
3	chr1:9828174..9830133-chr1:10270143..10271916,2	K562	blood:

Variant related genes	Relation type
ENSG00000054523	Chromatin interaction
ENSG00000171603	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10779730	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10779731	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10864436	0.85[EUR][1000 genomes]
rs10864437	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10864438	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11121489	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs11121490	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11121492	0.82[EUR][1000 genomes]
rs11121493	0.89[EUR][1000 genomes]
rs11674	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11804356	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs11806520	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12021914	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs12034239	0.86[EUR][1000 genomes]
rs12047054	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12064975	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs12078414	0.86[EUR][1000 genomes]
rs12087051	0.89[EUR][1000 genomes]
rs12088273	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1220419	0.80[ASN][1000 genomes]
rs1228434	0.89[EUR][1000 genomes]
rs12568720	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12569008	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1615629	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1631962	0.87[EUR][1000 genomes]
rs1660741	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1660742	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17034335	0.82[EUR][1000 genomes]
rs17034340	0.82[EUR][1000 genomes]
rs1767277	0.86[EUR][1000 genomes]
rs2788605	0.84[EUR][1000 genomes]
rs4512653	0.84[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs4585981	0.84[EUR][1000 genomes]
rs4845975	0.88[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs57560942	0.89[EUR][1000 genomes]
rs59729812	0.89[EUR][1000 genomes]
rs6699320	0.84[EUR][1000 genomes]
rs72855716	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72855733	0.82[EUR][1000 genomes]
rs72855735	0.84[EUR][1000 genomes]
rs72855745	0.89[EUR][1000 genomes]
rs72855747	0.89[EUR][1000 genomes]
rs7526958	0.98[ASN][1000 genomes]
rs7550246	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs767762	0.86[EUR][1000 genomes]
rs935071	0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3385337	chr1:9105242-10082223	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	549 gene(s)	inside rSNPs	diseases
2	nsv871610	chr1:9655795-10008221	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	esv3417409	chr1:9683992-10241703	Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
4	nsv832203	chr1:9726632-9860209	Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
5	nsv2298	chr1:9826286-9857487	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	esv3374230	chr1:9827590-9830088	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	esv3375592	chr1:9827590-9830138	Strong transcription Enhancers Weak transcription Genic enhancers ZNF genes & repeats	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
8	esv3404905	chr1:9828065-9829563	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:9801200-9837800	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr1:9801400-9854200	Weak transcription	Fetal Kidney	kidney
3	chr1:9804400-9836600	Weak transcription	Small Intestine	intestine
4	chr1:9804600-9836600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr1:9810000-9832400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr1:9810200-9829200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr1:9811600-9832400	Weak transcription	Primary hematopoietic stem cells	blood
8	chr1:9811600-9832400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr1:9811800-9832400	Weak transcription	Rectal Smooth Muscle	rectum
10	chr1:9811800-9857000	Weak transcription	Aorta	Aorta
11	chr1:9812400-9832200	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr1:9812600-9829000	Weak transcription	Stomach Mucosa	stomach
13	chr1:9812800-9831000	Weak transcription	Colon Smooth Muscle	Colon
14	chr1:9813400-9829000	Weak transcription	Colonic Mucosa	Colon
15	chr1:9813400-9830400	Weak transcription	GM12878-XiMat	blood
16	chr1:9813600-9831800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr1:9813600-9832400	Weak transcription	Right Ventricle	heart
18	chr1:9813800-9832400	Weak transcription	Adipose Nuclei	Adipose
19	chr1:9813800-9852200	Weak transcription	Right Atrium	heart
20	chr1:9815400-9829200	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr1:9815400-9831600	Weak transcription	Stomach Smooth Muscle	stomach
22	chr1:9815400-9832400	Weak transcription	Fetal Intestine Large	intestine
23	chr1:9815400-9832600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr1:9815600-9829600	Weak transcription	Primary T helper cells PMA-I stimulated	--
25	chr1:9815600-9830800	Weak transcription	Primary T helper cells fromperipheralblood	blood
26	chr1:9816400-9831800	Weak transcription	Brain Germinal Matrix	brain
27	chr1:9816600-9842400	Weak transcription	HUVEC	blood vessel
28	chr1:9820200-9832400	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr1:9820400-9831600	Weak transcription	Monocytes-CD14+_RO01746	blood
30	chr1:9820400-9832400	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr1:9820400-9832600	Weak transcription	Primary monocytes fromperipheralblood	blood
32	chr1:9820400-9832600	Weak transcription	Ovary	ovary
33	chr1:9820600-9832400	Weak transcription	Left Ventricle	heart
34	chr1:9820600-9832600	Weak transcription	Fetal Lung	lung
35	chr1:9820600-9836200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
36	chr1:9821000-9832400	Weak transcription	Esophagus	oesophagus
37	chr1:9821200-9829200	Weak transcription	Pancreas	Pancrea
38	chr1:9821200-9832400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr1:9821200-9832400	Weak transcription	HepG2	liver
40	chr1:9822000-9832400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr1:9822000-9832400	Weak transcription	HUES64 Cell Line	embryonic stem cell
42	chr1:9822000-9832400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
43	chr1:9822200-9829200	Weak transcription	Primary T cells fromperipheralblood	blood
44	chr1:9822200-9831800	Weak transcription	Placenta	Placenta
45	chr1:9822200-9844400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
46	chr1:9822400-9830600	Weak transcription	Fetal Muscle Leg	muscle
47	chr1:9822400-9832400	Weak transcription	Fetal Muscle Trunk	muscle
48	chr1:9822800-9832200	Weak transcription	Primary B cells from peripheral blood	blood
49	chr1:9822800-9832400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr1:9823800-9830600	Weak transcription	Rectal Mucosa Donor 29	rectum

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