Variant report

Variant	rs6678940
Chromosome Location	chr1:227062389-227062390
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:227056972..227060781-chr1:227061022..227064648,10	MCF-7	breast:
2	chr1:227060695..227062412-chr1:227077367..227078940,2	MCF-7	breast:
3	chr1:227061527..227064235-chr1:227072734..227074353,2	K562	blood:
4	chr1:227057812..227060402-chr1:227061799..227065310,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000143801	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs12069540	0.92[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs1341281	1.00[EUR][1000 genomes]
rs1341282	1.00[EUR][1000 genomes]
rs16846590	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4520384	1.00[EUR][1000 genomes]
rs4653463	1.00[JPT][hapmap]
rs57594469	1.00[EUR][1000 genomes]
rs58698650	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58973334	1.00[EUR][1000 genomes]
rs59683545	1.00[EUR][1000 genomes]
rs59692841	1.00[EUR][1000 genomes]
rs60294511	1.00[EUR][1000 genomes]
rs60560949	1.00[EUR][1000 genomes]
rs61103575	1.00[EUR][1000 genomes]
rs61185121	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6426539	1.00[EUR][1000 genomes]
rs6426540	1.00[EUR][1000 genomes]
rs6671059	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6675452	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6677908	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6678839	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74139805	1.00[EUR][1000 genomes]
rs74139806	1.00[EUR][1000 genomes]
rs7522645	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7523790	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7525819	0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7555672	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv4766	chr1:227025954-227070961	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv1003656	chr1:227034700-227559665	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer 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	35 gene(s)	inside rSNPs	diseases
3	nsv535318	chr1:227034700-227559665	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227059000-227066800	Weak transcription	Aorta	Aorta
2	chr1:227059200-227063600	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr1:227059200-227069000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr1:227059400-227063400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr1:227059400-227063400	Weak transcription	NH-A	brain
6	chr1:227059400-227069600	Weak transcription	Primary B cells from cord blood	blood
7	chr1:227059600-227063200	Weak transcription	NHEK	skin
8	chr1:227059600-227066000	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr1:227059600-227068400	Weak transcription	Brain Hippocampus Middle	brain
10	chr1:227059600-227069200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr1:227059600-227070200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr1:227059800-227062600	Weak transcription	Fetal Intestine Small	intestine
13	chr1:227059800-227062600	Weak transcription	Right Ventricle	heart
14	chr1:227059800-227063400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr1:227059800-227063400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
16	chr1:227059800-227063400	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr1:227059800-227063600	Weak transcription	Colonic Mucosa	Colon
18	chr1:227059800-227064400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr1:227059800-227064400	Weak transcription	Primary B cells from peripheral blood	blood
20	chr1:227059800-227064600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
21	chr1:227059800-227064600	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr1:227059800-227064600	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr1:227059800-227065000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr1:227059800-227067400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr1:227059800-227070200	Weak transcription	Osteobl	bone
26	chr1:227059800-227075600	Weak transcription	Brain Substantia Nigra	brain
27	chr1:227059800-227095000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr1:227060000-227063000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr1:227060000-227063200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr1:227060000-227063400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr1:227060000-227063400	Weak transcription	Stomach Smooth Muscle	stomach
32	chr1:227060000-227063800	Weak transcription	Brain Anterior Caudate	brain
33	chr1:227060000-227064600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr1:227060000-227064600	Weak transcription	Brain Cingulate Gyrus	brain
35	chr1:227060000-227064600	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr1:227060000-227065000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
37	chr1:227060000-227065000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr1:227060000-227065000	Weak transcription	HMEC	breast
39	chr1:227060000-227068200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr1:227060000-227068200	Weak transcription	Rectal Smooth Muscle	rectum
41	chr1:227060000-227068400	Weak transcription	Brain Angular Gyrus	brain
42	chr1:227060000-227068800	Weak transcription	NHDF-Ad	bronchial
43	chr1:227060000-227069400	Weak transcription	Esophagus	oesophagus
44	chr1:227060000-227069600	Weak transcription	Right Atrium	heart
45	chr1:227060000-227069800	Weak transcription	Monocytes-CD14+_RO01746	blood
46	chr1:227060000-227070000	Weak transcription	Small Intestine	intestine
47	chr1:227060000-227070600	Weak transcription	Fetal Brain Male	brain
48	chr1:227060200-227062800	Weak transcription	Pancreatic Islets	Pancreatic Islet
49	chr1:227060200-227070200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr1:227060400-227062600	Enhancers	Fetal Muscle Leg	muscle

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