Variant report

Variant	rs914156
Chromosome Location	chr21:40717478-40717479
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:24)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:24 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MXI1	chr21:40716967-40721099	SK-N-SH	brain:	n/a	n/a
2	POLR2A	chr21:40717375-40718296	SK-N-MC	brain:	n/a	n/a
3	POLR2A	chr21:40716894-40717482	GM12878	blood:	n/a	n/a
4	POLR2A	chr21:40717311-40718928	GM12891	blood:	n/a	n/a
5	POLR2A	chr21:40717293-40717681	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr21:40717202-40717918	HL-60	blood:	n/a	n/a
7	POLR2A	chr21:40716164-40723345	K562	blood:	n/a	n/a
8	POLR2A	chr21:40717140-40717512	HepG2	liver:	n/a	n/a
9	POLR2A	chr21:40717475-40717886	GM12891	blood:	n/a	n/a
10	POLR2A	chr21:40716823-40717879	GM12878	blood:	n/a	n/a
11	POLR2A	chr21:40717457-40717840	GM12892	blood:	n/a	n/a
12	POLR2A	chr21:40716871-40717588	GM12892	blood:	n/a	n/a
13	HEY1	chr21:40716930-40717871	K562	blood:	n/a	n/a
14	POLR2A	chr21:40716980-40717869	H1-hESC	embryonic stem cell:	n/a	n/a
15	POLR2A	chr21:40717406-40717562	ProgFib	skin:	n/a	n/a
16	POLR2A	chr21:40717080-40717821	HepG2	liver:	n/a	n/a
17	POLR2A	chr21:40716749-40718389	H1-hESC	embryonic stem cell:	n/a	n/a
18	POLR2A	chr21:40716913-40717827	GM12892	blood:	n/a	n/a
19	POLR2A	chr21:40717038-40717884	MCF-7	breast:	n/a	n/a
20	POLR2A	chr21:40716415-40718095	GM12878	blood:	n/a	n/a
21	POLR2A	chr21:40717284-40717793	HepG2	liver:	n/a	n/a
22	CUX1	chr21:40717377-40717552	K562	blood:	n/a	n/a
23	POLR2A	chr21:40717270-40717527	H1-hESC	embryonic stem cell:	n/a	n/a
24	POLR2A	chr21:40717227-40717522	H1-hESC	embryonic stem cell:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr21:40681596..40696529-chr21:40715399..40724266,46	K562	blood:
2	chr21:40716662..40723444-chr21:40748337..40754328,16	MCF-7	breast:
3	chr21:40635414..40638745-chr21:40717382..40720310,3	K562	blood:
4	chr21:40716442..40724032-chr21:40756185..40762223,18	K562	blood:
5	chr21:40652004..40654564-chr21:40716456..40719134,2	MCF-7	breast:
6	chr21:40716961..40722807-chr21:40750720..40754894,10	K562	blood:
7	chr21:40716961..40718462-chr21:40751682..40753726,2	K562	blood:
8	chr21:40716079..40725440-chr21:40756737..40764615,26	K562	blood:

No data

Variant related genes	Relation type
ENSG00000238556	TF binding region
ENSG00000255568	Chromatin interaction
ENSG00000185658	Chromatin interaction
ENSG00000182093	Chromatin interaction
ENSG00000238141	Chromatin interaction
ENSG00000227406	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs2026267	0.82[AFR][1000 genomes]
rs2249666	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2735307	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2735308	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2735309	0.82[AFR][1000 genomes]
rs2776306	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2776307	0.82[AFR][1000 genomes]
rs2776308	0.82[AFR][1000 genomes]
rs2776309	0.82[AFR][1000 genomes]
rs2776311	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2776312	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2854727	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2989329	0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3167757	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35123057	0.82[AFR][1000 genomes]
rs741795	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8128827	0.82[AFR][1000 genomes]
rs8128901	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8128919	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8132993	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9980890	0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][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	nsv913744	chr21:40670167-40757973	Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Weak transcription Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	53 gene(s)	inside rSNPs	diseases
2	nsv1059420	chr21:40684295-40745952	Flanking Active TSS Active TSS Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	50 gene(s)	inside rSNPs	diseases
3	nsv587483	chr21:40686327-40718161	Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
4	nsv1059868	chr21:40711535-41043291	Active TSS Enhancers Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs914156	HMGN1	Cis_1M	lymphoblastoid	RTeQTL
rs914156	HMGN1	cis	multi-tissue	Pritchard

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:40692400-40718400	Weak transcription	Right Atrium	heart
2	chr21:40704000-40719600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr21:40704600-40719600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr21:40711800-40719600	Weak transcription	Pancreas	Pancrea
5	chr21:40712200-40718800	Strong transcription	Fetal Muscle Trunk	muscle
6	chr21:40712600-40717600	Strong transcription	Primary neutrophils fromperipheralblood	blood
7	chr21:40712600-40717600	Strong transcription	Fetal Muscle Leg	muscle
8	chr21:40712600-40717600	Strong transcription	Rectal Mucosa Donor 29	rectum
9	chr21:40712600-40717600	Strong transcription	Thymus	Thymus
10	chr21:40712600-40718200	Strong transcription	HSMM	muscle
11	chr21:40712800-40717600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr21:40712800-40717600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
13	chr21:40712800-40717600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr21:40712800-40717600	Strong transcription	A549	lung
15	chr21:40712800-40717800	Strong transcription	Primary B cells from cord blood	blood
16	chr21:40712800-40717800	Strong transcription	Rectal Mucosa Donor 31	rectum
17	chr21:40712800-40718400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr21:40712800-40718600	Strong transcription	Primary B cells from peripheral blood	blood
19	chr21:40712800-40719200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr21:40712800-40719200	Strong transcription	Placenta	Placenta
21	chr21:40713000-40718800	Strong transcription	Skeletal Muscle Female	skeletal muscle
22	chr21:40713200-40717600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr21:40713600-40717600	Strong transcription	H9 Cell Line	embryonic stem cell
24	chr21:40713600-40718000	Strong transcription	Brain Hippocampus Middle	brain
25	chr21:40713600-40718600	Strong transcription	NHDF-Ad	bronchial
26	chr21:40714200-40718000	Weak transcription	Fetal Intestine Small	intestine
27	chr21:40715000-40719000	Strong transcription	Skeletal Muscle Male	skeletal muscle
28	chr21:40715200-40717600	Strong transcription	Sigmoid Colon	Sigmoid Colon
29	chr21:40715600-40719200	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
30	chr21:40715800-40717600	Weak transcription	Fetal Heart	heart
31	chr21:40715800-40717600	Weak transcription	Monocytes-CD14+_RO01746	blood
32	chr21:40715800-40718000	Weak transcription	HSMMtube	muscle
33	chr21:40715800-40718600	Weak transcription	Brain Cingulate Gyrus	brain
34	chr21:40715800-40718800	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr21:40715800-40719400	Weak transcription	Ovary	ovary
36	chr21:40715800-40719600	Weak transcription	Esophagus	oesophagus
37	chr21:40716000-40717600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr21:40716000-40717600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr21:40716000-40717600	Weak transcription	Stomach Smooth Muscle	stomach
40	chr21:40716000-40718200	Weak transcription	Adipose Nuclei	Adipose
41	chr21:40716000-40718400	Weak transcription	Duodenum Smooth Muscle	Duodenum
42	chr21:40716000-40718400	Weak transcription	Placenta Amnion	Placenta Amnion
43	chr21:40716000-40718600	Weak transcription	Brain Angular Gyrus	brain
44	chr21:40716000-40718600	Weak transcription	Brain Inferior Temporal Lobe	brain
45	chr21:40716000-40719400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr21:40716000-40719400	Weak transcription	Brain Anterior Caudate	brain
47	chr21:40716000-40719600	Weak transcription	Aorta	Aorta
48	chr21:40716000-40719600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
49	chr21:40716000-40719600	Weak transcription	Colonic Mucosa	Colon
50	chr21:40716000-40719600	Weak transcription	Gastric	stomach

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